Enhanced nucleic acid identification and detection

ABSTRACT

The present invention relates to assays, including amplification assays, conducted in the presence of modulators. These assays can be used to detect the presence of particular nucleic acid sequences. In particular, these assays can allow for genotyping or other genetic analysis.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No.15/030,202, filed Apr. 18, 2016, which is a U.S. National Phase patentapplication of PCT/US2014/060977, filed Oct. 16, 2014, which claims thebenefit of U.S. Provisional Application No. 61/893,051, filed Oct. 18,2013, U.S. Provisional Application No. 61/943,784, filed Feb. 24, 2014,U.S. Provisional Application No. 61/968,191, filed Mar. 20, 2014, U.S.Provisional Application No. 61/993,183, filed May 14, 2014, and U.S.Provisional Application No. 62/063,293, filed Oct. 13, 2014, all ofwhich are incorporated herein by reference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant No.OD003584, Grant No. EB012946, and Grant No. GM007616 awarded by theNational Institutes of Health and under Grant No. HR0011-11-2-0006awarded by DARPA. The government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Dec. 18, 2018, isnamed 42436_US_Sequence_Listing.txt and is 29,414 bytes in size.

BACKGROUND

Modern biological techniques, including nucleic acid analysis, offerpowerful tools for the analysis of samples. Samples from subjects andenvironmental sources can be analyzed for the presence of variouscompounds and organisms. Patients can be diagnosed for diseases,including infectious diseases and genetic diseases. Samples can begenotyped.

However, many analysis techniques require centralized laboratoryfacilities, trained technicians, sample preparation, refrigeration, andother resources. Such requirements can limit the utility of thesetechniques in point-of-care settings, limited resource settings, andother environments with difficult or no access to necessary resources.

SUMMARY

In some aspects, this disclosure provides a method comprising: (a)providing a first solution comprising a first nucleic acid and amodulator, wherein said modulator is capable of acting on said firstnucleic acid in a region amplified by an isothermal nucleic acidamplification reaction, thereby modulating said isothermal nucleic acidamplification reaction; (b) preparing a second solution comprising asecond nucleic acid and optionally comprising said modulator; and (c)conducting said isothermal nucleic acid amplification reaction in saidfirst solution and in said second solution.

In some aspects, this disclosure provides a method comprising: (a)providing a volume suspected of containing a target nucleic acidmolecule; and (b) conducting an isothermal nucleic acid amplificationreaction in said volume in the presence of a modulator, wherein saidmodulator modulates said nucleic acid amplification reaction in thepresence of said target nucleic acid molecule and wherein said modulatoracts on said target nucleic acid molecule within a region amplified bysaid isothermal nucleic acid amplification reaction.

In some aspects, this disclosure provides a method comprising: (a)providing a first volume comprising first nucleic acid and a secondvolume comprising second nucleic acid; (b) dispersing said first volumeamong a plurality of first areas such that said plurality of first areaseach comprise at most one copy of said first nucleic acid and dispersingsaid second volume among a plurality of second areas such that saidplurality of second areas each comprise at most one copy of said secondnucleic acid; (c) providing a modulator to said plurality of first areasor to said plurality of second areas, wherein said modulator modulates anucleic acid amplification reaction when in the presence of said firstnucleic acid; and (d) conducting said nucleic acid amplificationreaction in said plurality of first areas and said plurality of secondareas.

In some aspects, this disclosure provides a method comprising: (a)providing a volume suspected of containing target nucleic acidmolecules; (b) dispersing said volume among a plurality of areas, suchthat said plurality of areas each comprise at most one of said targetnucleic acid molecules; (c) providing a modulator to said plurality ofareas, wherein said modulator modulates a nucleic acid amplificationreaction in the presence of said target nucleic acid molecule; (d)conducting said nucleic acid amplification reaction in said plurality ofareas.

In some aspects, this disclosure provides a method comprising: (a)providing a first volume comprising first nucleic acid and a secondvolume comprising second nucleic acid; (b) dispersing said first volumeamong a plurality of first areas and dispersing said second volume amonga plurality of second areas; (c) providing a modulator to said pluralityof first areas or to said plurality of second areas, wherein saidmodulator modulates a nucleic acid amplification reaction when in thepresence of said first nucleic acid; and (d) conducting said nucleicacid amplification reaction in said plurality of first areas and in saidplurality of second areas, thereby producing positive amplificationsignal in a subset of said plurality of first areas.

In some aspects, this disclosure provides a method comprising: (a)providing a volume suspected of containing target nucleic acidmolecules; (b) dispersing said volume among a plurality of areas; (c)providing a modulator to said plurality of areas, wherein said modulatormodulates a nucleic acid amplification reaction in the presence of saidtarget nucleic acid molecule; (d) conducting said nucleic acidamplification reaction in said plurality of areas, thereby producingpositive amplification signal in a subset of said plurality of areas.

In some embodiments of aspects provided herein, the method furthercomprises detecting a difference in amplification between said firstnucleic acid and said second nucleic acid. In some embodiments ofaspects provided herein, said difference in amplification comprises adifference in amplification rate. In some embodiments of aspectsprovided herein, said difference in amplification comprises a differencein amplification efficiency. In some embodiments of aspects providedherein, said difference in amplification comprises a difference inamplification rate and a difference in amplification efficiency. In someembodiments of aspects provided herein, said detecting comprisesperforming sequencing. In some embodiments of aspects provided herein,said detecting does not comprise performing sequencing. In someembodiments of aspects provided herein, said detecting comprises massspectrometry. In some embodiments of aspects provided herein, saiddetecting does not comprise mass spectrometry. In some embodiments ofaspects provided herein, said detecting comprises performingelectrophoresis. In some embodiments of aspects provided herein, saiddetecting does not comprise performing electrophoresis. In someembodiments of aspects provided herein, said providing a modulator ofstep (c) occurs before said dispersing of step (b). In some embodimentsof aspects provided herein, said providing a modulator of step (c)occurs during said dispersing of step (b). In some embodiments ofaspects provided herein, said providing a modulator of step (c) occursafter said dispersing of step (b). In some embodiments of aspectsprovided herein, the method further comprises dispersing said firstvolume among a plurality of third areas such that said plurality ofthird areas each comprise more than one copy of said first nucleic acidand dispersing said second volume among a plurality of fourth areas suchthat said plurality of fourth areas each comprise more than one copy ofsaid second nucleic acid. In some embodiments of aspects providedherein, the method further comprises dispersing said volume among asecond plurality of areas, such that said second plurality of areas eachcomprise more than one of said target nucleic acid molecules. In someembodiments of aspects provided herein, said modulator acts during saidnucleic acid amplification reaction. In some embodiments of aspectsprovided herein, said modulator acts before said nucleic acidamplification reaction. In some embodiments of aspects provided herein,said modulator acts after said nucleic acid amplification reaction. Insome embodiments of aspects provided herein, said modulator acts byinhibiting said nucleic acid amplification reaction. In some embodimentsof aspects provided herein, said modulator acts by promoting saidnucleic acid amplification reaction. In some embodiments of aspectsprovided herein, said modulator acts by promoting said nucleic acidamplification reaction by inhibiting off-target reactions. In someembodiments of aspects provided herein, said nucleic acid amplificationreaction comprises an isothermal amplification reaction. In someembodiments of aspects provided herein, said isothermal nucleic acidamplification reaction is performed in a digital format. In someembodiments of aspects provided herein, said modulator acts on a nucleicacid outside of a priming region of said nucleic acid amplificationreaction. In some embodiments of aspects provided herein, said modulatoracts on a nucleic acid inside a priming region of said nucleic acidamplification reaction. In some embodiments of aspects provided herein,said modulator comprises an enzyme. In some embodiments of aspectsprovided herein, said modulator comprises an enzyme that acts on nucleicacids in a sequence-targeted manner. In some embodiments of aspectsprovided herein, said modulator binds a nucleic acid molecule in asequence-targeted manner. In some embodiments of aspects providedherein, said modulator acts on nucleic acids in a methylation-targetedmanner. In some embodiments of aspects provided herein, said modulatoracts on nucleic acids in a glycosylation-targeted manner. In someembodiments of aspects provided herein, said modulator comprises arestriction enzyme. In some embodiments of aspects provided herein, saidmodulator comprises a nucleic acid modifying enzyme. In some embodimentsof aspects provided herein, said modulator comprises a ligase. In someembodiments of aspects provided herein, said modulator comprises anengineered or non-natural nuclease. In some embodiments of aspectsprovided herein, said modulator comprises a modulator selected from thegroup consisting of zinc-finger nuclease, transcription activator-likeeffector nuclease, meganuclease, and RNA-guided Cas9 nuclease. In someembodiments of aspects provided herein, said modulator comprises anoligonucleotide. In some embodiments of aspects provided herein, saidmodulator comprises an artificial nucleic acid or a nucleic acid analog.In some embodiments of aspects provided herein, said modulator comprisespeptide nucleic acid (PNA), locked nucleic acid (LNA), inosine, ordideoxynucleotide (ddNTP). In some embodiments of aspects providedherein, said modulator comprises an oligonucleotide comprising modifiedbases or unnatural bases. In some embodiments of aspects providedherein, said modulator comprises a repair protein. In some embodimentsof aspects provided herein, said modulator comprises a repair proteinselected from the group consisting of MutH, MutL, and MutS. In someembodiments of aspects provided herein, said modulator promotes saidnucleic acid amplification reaction by affecting secondary structures.In some embodiments of aspects provided herein, said modulator competeswith primers for said nucleic acid amplification reaction. In someembodiments of aspects provided herein, said modulator is inactive untilactivation by an enzymatic activity. In some embodiments of aspectsprovided herein, said conducting occurs on a microfluidic device. Insome embodiments of aspects provided herein, said conducting occurs on amicrowell plate. In some embodiments of aspects provided herein, saidconducting occurs on a solid support. In some embodiments of aspectsprovided herein, said conducting occurs not on a solid support. In someembodiments of aspects provided herein, said conducting occurs inmicrofluidic droplets. In some embodiments of aspects provided herein,said conducting occurs in an emulsion.

In some aspects, this disclosure provides a method comprising: (a)providing a volume suspected of containing a first target nucleic acidmolecule; (b) conducting a first nucleic acid amplification reaction ona first part of said volume in the presence of a first modulator,wherein said first modulator modulates said first nucleic acidamplification reaction in the presence of said first target nucleic acidmolecule; (c) conducting a second nucleic acid amplification reaction ona second part of said volume, optionally in the presence of a secondmodulator, wherein said second modulator, if present, modulates saidsecond nucleic acid amplification reaction in the presence of a secondtarget nucleic acid molecule; (d) generating a modulated amplificationpattern based on results from said first nucleic acid amplificationreaction and said second nucleic acid amplification reaction; and (e)comparing said modulated amplification pattern to a reference pattern.

In some embodiments of aspects provided herein, said results compriseamplification rate results. In some embodiments of aspects providedherein, said results comprise amplification efficiency results. In someembodiments of aspects provided herein, said results compriseamplification rate results and amplification efficiency results. In someembodiments of aspects provided herein, said generating does notcomprise gel electrophoresis. In some embodiments of aspects providedherein, said first modulator or said second modulator acts during saidnucleic acid amplification reaction. In some embodiments of aspectsprovided herein, said first modulator or said second modulator actsbefore said nucleic acid amplification reaction. In some embodiments ofaspects provided herein, said first modulator or said second modulatoracts after said nucleic acid amplification reaction. In some embodimentsof aspects provided herein, said first modulator or said secondmodulator acts by inhibiting said nucleic acid amplification reaction.In some embodiments of aspects provided herein, said first modulator orsaid second modulator acts by promoting said nucleic acid amplificationreaction. In some embodiments of aspects provided herein, said firstmodulator or said second modulator acts by promoting said nucleic acidamplification reaction by inhibiting off-target reactions. In someembodiments of aspects provided herein, said first nucleic acidamplification reaction or said second nucleic acid amplificationreaction comprises an isothermal amplification reaction. In someembodiments of aspects provided herein, said first nucleic acidamplification reaction or said second nucleic acid amplification isperformed in a digital format. In some embodiments of aspects providedherein, said first modulator or said second modulator acts on a nucleicacid outside of a priming region of said nucleic acid amplificationreaction. In some embodiments of aspects provided herein, said firstmodulator or said second modulator comprises an enzyme. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator comprises an enzyme that acts on nucleic acids in asequence-targeted manner. In some embodiments of aspects providedherein, said first modulator or said second modulator binds a nucleicacid molecule in a sequence-targeted manner. In some embodiments ofaspects provided herein, said first modulator or said second modulatoracts on nucleic acids in a methylation-targeted manner. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator acts on nucleic acids in a glycosylation-targetedmanner. In some embodiments of aspects provided herein, said firstmodulator or said second modulator comprises a restriction enzyme. Insome embodiments of aspects provided herein, said first modulator orsaid second modulator comprises a nucleic acid modifying enzyme. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator comprises a ligase. In some embodiments of aspectsprovided herein, said first modulator or said second modulator comprisesan engineered or non-natural nuclease. In some embodiments of aspectsprovided herein, said first modulator or said second modulator comprisesa modulator selected from the group consisting of zinc-finger nuclease,transcription activator-like effector nuclease, meganuclease, andRNA-guided Cas9 nuclease. In some embodiments of aspects providedherein, said first modulator or said second modulator comprises anoligonucleotide. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator comprises an artificial nucleicacid or a nucleic acid analog. In some embodiments of aspects providedherein, said first modulator or said second modulator comprises peptidenucleic acid (PNA), locked nucleic acid (LNA), inosine, ordideoxynucleotide (ddNTP). In some embodiments of aspects providedherein, said first modulator or said second modulator comprises anoligonucleotide comprising modified bases or unnatural bases. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator comprises a repair protein. In some embodiments ofaspects provided herein, said first modulator or said second modulatorcomprises a repair protein selected from the group consisting of MutH,MutL, and MutS. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator promotes said nucleic acidamplification reaction by affecting secondary structures. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator competes with primers for said nucleic acidamplification reaction. In some embodiments of aspects provided herein,said first modulator or said second modulator is inactive untilactivation by an enzymatic activity. In some embodiments of aspectsprovided herein, said conducting a first nucleic acid amplificationreaction or said conducting a second nucleic acid amplification reactionoccurs on a microfluidic device. In some embodiments of aspects providedherein, said conducting a first nucleic acid amplification reaction orsaid conducting a second nucleic acid amplification reaction occurs on amicrowell plate. In some embodiments of aspects provided herein, saidconducting a first nucleic acid amplification reaction or saidconducting a second nucleic acid amplification reaction occurs on asolid support. In some embodiments of aspects provided herein, saidconducting a first nucleic acid amplification reaction or saidconducting a second nucleic acid amplification reaction occurs not on asolid support. In some embodiments of aspects provided herein, saidconducting a first nucleic acid amplification reaction or saidconducting a second nucleic acid amplification reaction occurs inmicrofluidic droplets. In some embodiments of aspects provided herein,said conducting a first nucleic acid amplification reaction or saidconducting a second nucleic acid amplification reaction occurs in anemulsion.

In some aspects, this disclosure provides a method comprising: (a)providing a first volume comprising a first nucleic acid and a secondvolume comprising a second nucleic acid; (b) dispersing said firstvolume among a plurality of first areas; (c) dispersing said secondvolume among a plurality of second areas; (d) providing a modulator tosaid plurality of first areas or to said plurality of second areas; and(e) conducting said nucleic acid amplification reaction, therebyproducing a positive signal in a subset of said plurality of firstareas, wherein said modulator modulates said producing when in thepresence of said first nucleic acid.

In some aspects, this disclosure provides a method comprising: (a)providing a volume suspected of containing a target nucleic acidmolecule; (b) dispersing said volume among a plurality of areas; (c)dispersing a modulator among said plurality of areas; (c) conductingsaid nucleic acid amplification reaction in said plurality of areas,thereby producing a positive amplification signal in a subset of saidplurality of areas, wherein said modulator modulates said producing whenin the presence of said target nucleic acid molecule.

In some embodiments of aspects provided herein, said producing comprisesproducing fluorescence. In some embodiments of aspects provided herein,said producing comprises producing a precipitate. In some embodiments ofaspects provided herein, said producing comprises producing a gasbubble. In some embodiments of aspects provided herein, said producingcomprises conducting nucleic acid sequencing. In some embodiments ofaspects provided herein, said producing comprises conducting massspectrometry. In some embodiments of aspects provided herein, saidproducing comprises quenching. In some embodiments of aspects providedherein, said modulator comprises an enzyme. In some embodiments ofaspects provided herein, said modulator comprises an enzyme that acts onnucleic acids in a sequence-targeted manner. In some embodiments ofaspects provided herein, said modulator binds a nucleic acid molecule ina sequence-targeted manner. In some embodiments of aspects providedherein, said modulator acts on nucleic acids in a methylation-targetedmanner. In some embodiments of aspects provided herein, said modulatoracts on nucleic acids in a glycosylation-targeted manner. In someembodiments of aspects provided herein, said modulator comprises arestriction enzyme. In some embodiments of aspects provided herein, saidmodulator comprises a nucleic acid modifying enzyme. In some embodimentsof aspects provided herein, said modulator comprises a ligase. In someembodiments of aspects provided herein, said modulator comprises anengineered or non-natural nuclease. In some embodiments of aspectsprovided herein, said modulator comprises a modulator selected from thegroup consisting of zinc-finger nuclease, transcription activator-likeeffector nuclease, meganuclease, and RNA-guided Cas9 nuclease. In someembodiments of aspects provided herein, said modulator comprises anoligonucleotide. In some embodiments of aspects provided herein, saidmodulator comprises an artificial nucleic acid or a nucleic acid analog.In some embodiments of aspects provided herein, said modulator comprisespeptide nucleic acid (PNA), locked nucleic acid (LNA), inosine, ordideoxynucleotide (ddNTP). In some embodiments of aspects providedherein, said modulator comprises an oligonucleotide comprising modifiedbases or unnatural bases. In some embodiments of aspects providedherein, said modulator comprises a repair protein. In some embodimentsof aspects provided herein, said modulator comprises a repair proteinselected from the group consisting of MutH, MutL, and MutS. In someembodiments of aspects provided herein, said modulator promotes saidnucleic acid amplification reaction by affecting secondary structures.In some embodiments of aspects provided herein, said modulator competeswith primers for said nucleic acid amplification reaction. In someembodiments of aspects provided herein, said modulator is inactive untilactivation by an enzymatic activity. In some embodiments of aspectsprovided herein, said conducting occurs on a microfluidic device. Insome embodiments of aspects provided herein, said conducting occurs on amicrowell plate. In some embodiments of aspects provided herein, saidconducting occurs on a solid support. In some embodiments of aspectsprovided herein, said conducting occurs not on a solid support. In someembodiments of aspects provided herein, said conducting occurs inmicrofluidic droplets. In some embodiments of aspects provided herein,said conducting occurs in an emulsion. In some embodiments of aspectsprovided herein, said nucleic acid amplification reaction is conductedin a digital format. In some embodiments of aspects provided herein,said nucleic acid amplification reaction comprises an isothermal nucleicacid amplification reaction.

In some aspects, this disclosure provides a method comprising: (a)providing a volume comprising first reagents for a first reaction andsecond reagents for a second reaction; (b) conducting said firstreaction and said second reaction; and (c) observing results from saidfirst reaction, thereby determining the relative rate or relativeefficiency of said first reaction and said second reaction.

In some aspects, this disclosure provides a method comprising: (a)providing a volume comprising first reagents for a first reaction secondreagents for a second reaction; (b) dispersing said volume among aplurality of areas; and (c) conducting said first reaction and saidsecond reaction in said plurality of areas, thereby producing positivesignal in a subset of said plurality of first areas.

In some embodiments of aspects provided herein, said conducting occurson a microfluidic device. In some embodiments of aspects providedherein, said conducting occurs on a microwell plate. In some embodimentsof aspects provided herein, said conducting occurs on a solid support.In some embodiments of aspects provided herein, said conducting occursnot on a solid support. In some embodiments of aspects provided herein,said conducting occurs in microfluidic droplets. In some embodiments ofaspects provided herein, said conducting occurs in an emulsion. In someembodiments of aspects provided herein, said conducting occurs in adigital format. In some embodiments of aspects provided herein, saidreaction, said first reaction, or said second reaction comprise anisothermal reaction.

In some aspects, this disclosure provides a device comprising: (a) asample inlet; (b) a reaction chamber; (c) a first modulator; and (d) afluid handling component, wherein said fluid handling component ispositioned to combine said first modulator with a portion of a samplecomprising an analyte loaded in said sample inlet.

In some embodiments of aspects provided herein, the device furthercomprises a second modulator. In some embodiments of aspects providedherein, the device further comprises amplification reaction reagents. Insome embodiments of aspects provided herein, said amplification reactionreagents comprise isothermal amplification reaction reagents. In someembodiments of aspects provided herein, the device further comprises asample preparation module. In some embodiments of aspects providedherein, the device further comprises a detector. In some embodiments ofaspects provided herein, said first modulator or said second modulatorcomprises an enzyme. In some embodiments of aspects provided herein,said first modulator or said second modulator comprises an enzyme thatacts on nucleic acids in a sequence-targeted manner. In some embodimentsof aspects provided herein, said first modulator or said secondmodulator binds a nucleic acid molecule in a sequence-targeted manner.In some embodiments of aspects provided herein, said first modulator orsaid second modulator acts on nucleic acids in a methylation-targetedmanner. In some embodiments of aspects provided herein, said firstmodulator or said second modulator acts on nucleic acids in aglycosylation-targeted manner. In some embodiments of aspects providedherein, said first modulator or said second modulator comprises arestriction enzyme. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator comprises a nucleic acidmodifying enzyme. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator comprises a ligase. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator comprises an engineered or non-natural nuclease. Insome embodiments of aspects provided herein, said first modulator orsaid second modulator comprises a first modulator or said secondmodulator selected from the group consisting of zinc-finger nuclease,transcription activator-like effector nuclease, meganuclease, andRNA-guided Cas9 nuclease. In some embodiments of aspects providedherein, said first modulator or said second modulator comprises anoligonucleotide. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator comprises an artificial nucleicacid or a nucleic acid analog. In some embodiments of aspects providedherein, said first modulator or said second modulator comprises peptidenucleic acid (PNA), locked nucleic acid (LNA), inosine, ordideoxynucleotide (ddNTP). In some embodiments of aspects providedherein, said first modulator or said second modulator comprises anoligonucleotide comprising modified bases or unnatural bases. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator comprises a repair protein. In some embodiments ofaspects provided herein, said first modulator or said second modulatorcomprises a repair protein selected from the group consisting of MutH,MutL, and MutS. In some embodiments of aspects provided herein, saidfirst modulator or said second modulator promotes said nucleic acidamplification reaction by affecting secondary structures. In someembodiments of aspects provided herein, said first modulator or saidsecond modulator competes with primers for said nucleic acidamplification reaction. In some embodiments of aspects provided herein,said first modulator or said second modulator is inactive untilactivation by an enzymatic activity. In some embodiments of aspectsprovided herein, said device comprises a microfluidic device. In someembodiments of aspects provided herein, said device comprises amicrowell plate. In some embodiments of aspects provided herein, saiddevice comprises a solid support. In some embodiments of aspectsprovided herein, said device does not comprise a solid support. In someembodiments of aspects provided herein, said device comprises amicrofluidic droplet generator. In some embodiments of aspects providedherein, said device comprises an emulsion generator. In some embodimentsof aspects provided herein, said fluid handling component is configuredto provide said portion of said sample to said reaction chamber suchthat said reaction chamber comprises at most one copy of said analyte.In some embodiments of aspects provided herein, said analyte comprises anucleic acid. In some embodiments of aspects provided herein, saidanalyte comprises DNA. In some embodiments of aspects provided herein,said analyte comprises RNA.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference in their entiretiesfor all purposes to the same extent as if each individual publication,patent, or patent application was specifically and individuallyindicated to be incorporated by reference in its entirety for allpurposes.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 shows an exemplary schematic of an assay design.

FIG. 2A shows an exemplary schematic illustrating the possible outcomeand rate of an amplification reaction.

FIG. 2B shows an exemplary schematic illustrating the possible outcomeand rate of a nucleic acid amplification reaction in the presence of arestriction enzyme.

FIG. 3A shows an exemplary schematic of an assay comprising the sameprimer set and a different restriction enzyme in each compartment.

FIG. 3B shows an exemplary schematic of an assay comprising a differentprimer set and the same restriction enzyme in each compartment.

FIG. 3C shows an exemplary schematic of an assay comprising a differentrestriction enzyme in each column of compartments and a different primerset in each row of compartments.

FIG. 3D shows an exemplary schematic of each compartment further dividedinto smaller compartments to perform digital amplification or detection.

FIG. 4 shows an exemplary schematic of a NASBA amplification reaction.

FIG. 5A shows an exemplary alignment of RNA sequence, priming region anddigestion site for NheI, BstNI, BsrBI, BsrI, and BcoDI.

FIG. 5B shows an exemplary alignment of RNA sequence and potentialdigestion site for 1a 1b subtyping in core region of HCV.

FIG. 6 shows a computer system 601 that is programmed or otherwiseconfigured to regulate or analyze assays.

FIG. 7 shows an exemplary predicted amplification pattern.

FIG. 8 shows exemplary results for time to positive from an assay.

FIG. 9 shows exemplary results for number of counts from an assay.

FIG. 10 shows exemplary digital RT-LAMP results on a SlipChip platform.

FIG. 11A shows exemplary results for real-time digital and bulkamplification of HCV genotype 1 with and without NheI.

FIG. 11B shows exemplary results for real-time digital and bulkamplification of HCV genotype 1 with and without BsrBI.

FIG. 11C shows exemplary results for real-time digital and bulkamplification of HCV genotype 1 with and without BstNI.

FIG. 11D shows exemplary results for real-time digital and bulkamplification of HCV genotype 2 with and without NheI.

FIG. 11E shows exemplary results for real-time digital and bulkamplification of HCV genotype 2 with and without BsrBI.

FIG. 11F shows exemplary results for real-time digital and bulkamplification of HCV genotype 2 with and without BstNI.

FIG. 11G shows exemplary results for real-time digital and bulkamplification of HCV genotype 3 with and without NheI.

FIG. 11H shows exemplary results for real-time digital and bulkamplification of HCV genotype 3 with and without BsrBI.

FIG. 11I shows exemplary results for real-time digital and bulkamplification of HCV genotype 3 with and without BstNI.

FIG. 11J shows exemplary results for real-time digital and bulkamplification of HCV genotype 4 with and without NheI.

FIG. 11K shows exemplary results for real-time digital and bulkamplification of HCV genotype 4 with and without BsrBI.

FIG. 11L shows exemplary results for real-time digital and bulkamplification of HCV genotype 4 with and without BstNI.

FIG. 12A shows exemplary results from digital RT-LAMP for HCV RNAGenotype 1 with a matched inhibitor on a SlipChip device.

FIG. 12B shows exemplary results from digital RT-LAMP for HCV RNAGenotype 1 with a mismatched inhibitor on a SlipChip device.

FIG. 12C shows exemplary results from digital RT-LAMP for HCV RNAGenotype 1 with no inhibitor on a SlipChip device.

FIG. 13 shows exemplary alignment of RNA sequences for genotypes 1, 2, 3and 4, priming and molecular beacon probe regions, and digestion sitesof NheI, BsrBI, ApoI, BsrGI, NruI (or Bsp681), BseYI and BstXI.

FIG. 14 shows exemplary expected amplification results from an assay.

FIG. 15 shows exemplary results for the time required for NASBA reactionto change from negative.

FIG. 16A shows an exemplary design and expected results for an assay fortrisomy.

FIG. 16B shows an exemplary design and expected results for an assay fortrisomy.

FIG. 17 shows an exemplary illustration of B side primer and primer partsequence variants (Seq ID Nos: 70-72 and 51) aligned to a typical HCVsequence (Seq ID No: 94, Seq ID No: 95) shown together with amino acidsequences encoded thereby (Seq ID No: 96, and Seq ID No: 97).

FIG. 18 shows an exemplary illustration of F side primer and primer partsequence variants (Seq ID No: 43, Seq ID No: 44, Seq ID No: 73 and SeqID No: 74) aligned to a typical HCV sequence (Seq ID No: 98, Seq ID No:99) shown together with amino acid sequences encoded thereby (Seq ID No:100, and Seq ID No: 101).

FIG. 19 shows exemplary results for the number of positive wells versustime from a one-step dRT-LAMP HCV RNA detection assay.

FIG. 20 shows exemplary results for the signal from each well versustime from a one-step dRT-LAMP HCV RNA detection assay.

FIG. 21 shows an exemplary image of a SlipChip device with results froma one-step dRT-LAMP HCV RNA detection assay.

FIG. 22A shows exemplary results for the number of positive wells versustime from a one-step dRT-LAMP HCV RNA detection assay.

FIG. 22B shows exemplary results for the number of positive wells versustime from a one-step dRT-LAMP HCV RNA detection assay.

FIG. 23 shows exemplary results comparing time to positive for differentrestriction enzymes at different dilutions.

FIG. 24A shows an exemplary schematic of a SlipChip device top andbottom.

FIG. 24B shows an exemplary schematic of a SlipChip device aligned forloading.

FIG. 24C shows an exemplary schematic of a SlipChip device aligned forcompartmentalization.

FIG. 25A shows exemplary results for 1280 fluorescence traces for theRT-LAMP amplification process of all the wells on a SlipChip device(solid lines) and normalized averaged fluorescence curve in bulk (dashedline) in the absence of restriction enzymes.

FIG. 25B shows exemplary results for traces for a digital assay (solidlines) and for a bulk assay (dashed line) in the presence of restrictionenzyme BsrBI.

FIG. 25C shows exemplary results for the change of cumulative countsover time for wells exceeding the threshold in FIG. 25A, (upper fivelines), and FIG. 25B (lower lines).

FIG. 26 shows an exemplary histogram of real-time, single-moleculedigital RT-LAMP/RE experiments for HCV GT1 RNA.

FIG. 27A shows exemplary real-time RT-LAMP curves for GT1 in the absenceof restriction enzyme (positive control).

FIG. 27B shows exemplary real-time RT-LAMP curves for GT1 in thepresence of BsrBI.

FIG. 28A shows exemplary predicted results for an amplification reactionassay with different restriction enzymes and genotypes.

FIG. 28B shows exemplary experimental results on a device for anamplification reaction assay with different restriction enzymes andgenotypes.

FIG. 29A shows exemplary experimental results in an electrophoresis gelfor an amplification reaction assay with different restriction enzymesand genotypes.

FIG. 29B shows exemplary predicted results for an amplification reactionassay with different restriction enzymes and genotypes.

FIG. 30A shows exemplary results from a real-time bulk format HCVgenotyping assay.

FIG. 30B shows exemplary results from a digital format HCV genotypingassay.

FIG. 31A shows exemplary results from a digital format HCV genotypingassay for genotype 3 without a restriction enzyme, conducted on aSlipChip device.

FIG. 31B shows exemplary results from a digital format HCV genotypingassay for genotype 3 with BsrBI, conducted on a SlipChip device.

FIG. 31C shows exemplary results from a digital format HCV genotypingassay for genotype 1 with BsrBI, conducted on a SlipChip device.

FIG. 31D shows exemplary results from a digital format HCV genotypingassay for genotype 3 with BstNI, conducted on a SlipChip device.

FIG. 32A shows exemplary results from performance of a NASBA reactionusing a DNA molecular beacon (dashed line) and RNA molecular beacon(solid line) with standard concentration of RNase H.

FIG. 32B shows exemplary results from performance of a NASBA reactionusing a DNA molecular beacon (dashed line) and RNA molecular beacon(solid line) with increased concentration of RNase H.

FIG. 33A shows exemplary results for mean time to positive from amodified NASBA reaction.

FIG. 33B shows exemplary results for mean final fluorescent intensityfrom a modified NASBA reaction.

FIG. 34A shows a graph of exemplary results from experiments on theeffect of preincubation on the time to positive of restriction enzyme(ApoI) enhanced RNA NASBA compared to regular NASBA.

FIG. 34B shows exemplary results in an electrophoresis gel fromexperiments on the effect of preincubation on the time to positive ofrestriction enzyme (ApoI) enhanced RNA NASBA compared to regular NASBA

DETAILED DESCRIPTION

Overview

Herein described are approaches, devices and methods that can be used tocontrol a process, such as a detection or an amplification reaction, byadding a modulator. A modulator can be an external substance that canproduce a modulating (positive or negative) effect to the process (e.g.,amplification) and can change (increase or decrease) one or more fromthe following: the rate of the process, the efficiency of the process,the amount of product, the identity of the product, or changes in thedetection outcome. A modulator can be an inhibitor, producing a negativemodulating effect. A modulator can be a promoter, producing a positivemodulating effect. Detection can include detection by amplification,sequencing, mass spectrometry, electrophoresis, and others, as well asprocesses used as part of detection, such as reverse transcription;methods described herein can be used to impact these processes.

In some cases, processes (e.g. detection and/or amplification reactions)can be inhibited by the action of the modulator, such as restrictionenzyme or restriction endonuclease (RE) or other nucleic acid modifyingenzymes. For example, restriction enzymes can cleave templates orproducts of amplification or reverse transcription reactions. In somecases, a modulator can comprise a modified oligonucleotide (“oligo”).Isothermal amplification processes can provide advantages in these andother cases to broaden the range of inhibitors available for use toinhibit the process. In some examples, RNA-guided Cas9 nucleases fromCRISPR system or peptide nucleic acid (PNA) can be used. In someexamples, restriction enzymes (RE) can be used to control the process ofRT-LAMP amplification to perform genotyping (e.g. HCV genotyping).

FIG. 1 shows an exemplary schematic of an assay design usingamplification in the presence of restriction enzymes to genotypehepatitis C virus (HCV) RNA. Solid lines between genotypes (ovals, leftside) and restriction enzymes (rectangles, right side) representinhibition feedback and dashed lines represent lack of inhibitionfeedback. By conducting amplification reactions on a sample in thepresence or absence of different restriction enzymes, the sample'sgenotype can be determined based on which inhibitors recognize thesample nucleic acid and therefore inhibit its amplification.

FIG. 2 shows a schematic illustrating the possible outcome (“fate”) andrate of an amplification reaction. FIG. 2A shows a starting molecule(top) with two possible outcomes or fates—no amplification (left path)and amplification (right path). If the molecule undergoes amplification,the rate of amplification can also be measured. FIG. 2B shows a startingnucleic acid molecule (top) with two possible outcomes or fates in thepresence of a restriction enzyme—amplification (left path) or noamplification (right path). If the molecule undergoes amplification, therate of amplification can also be measured.

In some cases, a ligation reaction (e.g., using a ligase) can beperformed in combination with an amplification reaction, leading, forexample, to the detection of the ligated product. In some cases, amodulator can modulate a ligation reaction. For example, a restrictionenzyme can digest template or product of a ligation reaction.

The approaches, methods, and devices disclosed herein can providedifferent advantages. In some cases, methods can be used that do notrequire post-amplification digestion. In some cases, methods can be usedthat do not require electrophoresis, such as gel electrophoresis orcapillary electrophoresis. In some cases, modulators (e.g., restrictionenzymes, oligonucleotides) can provide specificity, such as byrecognizing specific nucleotide sequences. In some cases, the method canprovide high sensitivity, including single molecule sensitivity.Approaches, devices and methods disclosed herein can be used to producenucleic acids for subsequent uses. Methods disclosed herein can comprisethe detection, quantification, production, or degradation of one or morenucleic acids, including in a sequence-targeted or sequence-specificmanner Methods disclosed herein can comprise detection or quantificationof a single nucleotide polymorphism (SNP), a genotype of an allele,modifications of nucleic acid bases, molecules that interact withnucleic acids (including in a sequence-targeted or sequence specificmanner), transcription factors, DNA-binding proteins, histones,oligonucleotides, or enzymes that interact with nucleic acids (includingin a sequence-targeted or sequence specific manner). Methods disclosedherein can comprise homogeneous reactions. Methods disclosed herein cancomprise one-step reactions or one-pot reactions. Methods disclosedherein can comprise providing a direct read-out.

The present application incorporates the following applications byreference in their entireties for any and all purposes: U.S. Application61/516,628, “Digital Isothermal Quantification of Nucleic Acids ViaSimultaneous Chemical Initiation of Recombinase Polymerase Amplification(RPA) Reactions on Slip Chip,” filed on Apr. 5, 2011; U.S. Application61/518,601, “Quantification of Nucleic Acids With Large Dynamic RangeUsing Multivolume Digital Reverse Transcription PCR (RT-PCR) On ARotational Slip Chip Tested With Viral Load,” filed on May 9, 2011; U.S.application Ser. No. 13/257,811, “Slip Chip Device and Methods,” filedon Sep. 20, 2011; international application PCT/US2010/028361, “SlipChip Device and Methods,” filed on Mar. 23, 2010; U.S. Application61/262,375, “Slip Chip Device and Methods,” filed on Nov. 18, 2009; U.S.Application 61/162,922, “Sip Chip Device and Methods,” filed on Mar. 24,2009; U.S. Application 61/340,872, “Slip Chip Device and Methods,” filedon Mar. 22, 2010; U.S. application Ser. No. 13/440,371, “AnalysisDevices, Kits, And Related Methods For Digital Quantification Of NucleicAcids And Other Analytes,” filed on Apr. 5, 2012; and U.S. applicationSer. No. 13/467,482, “Multivolume Devices, Kits, Related Methods forQuantification and Detection of Nucleic Acids and Other Analytes,” filedon May 9, 2012; U.S. application Ser. No. 13/868,028, “Fluidic Devicesand Systems for Sample Preparation or Autonomous Analysis,” filed onApr. 22, 2013; U.S. application Ser. No. 13/868,009, “Fluidic Devicesfor Biospecimen Preservation,” filed on Apr. 22, 2013; and internationalapplication PCT/US13/63594, “Methods and Systems for MicrofluidicsImaging and Analysis,” filed on Oct. 4, 2013.

The term “or” as used herein is generally meant inclusively.

The term “about” as used herein means+/−10% of the recited value.

Reaction Chemistries

The process to be modulated can comprise one or more reactions,including but not limited to nucleic acid amplification, reversetranscription, digestion, cloning, ligation, hybridization,phosphorylation, dephosphorylation, glycosylation, deglycosylation,ubiquitination, deubiquitination, S-nitrosylation, denistrosylation,methylation, demethylation, N-acetylation, deacetylation, lipidation,proteolysis, sequencing, or signal generation.

Nucleic Acid Amplification

The process to be modulated can comprise nucleic acid amplification.Various nucleic acid amplification methods can be used. Modulationmethods using restriction enzymes can use nucleic acid amplificationmethods wherein the amplification conditions allow the activity of therestriction enzyme to be preserved or partially preserved. The nucleicacid amplification method can comprise polymerase chain reaction (PCR),reverse transcription PCR (RT-PCR), quantitative PCR (qPCR), reversetranscription qPCR (RT-qPCR), nested PCR, multiplex PCR, asymmetric PCR,touchdown PCR, random primer PCR, hemi-nested PCR, polymerase cyclingassembly (PCA), colony PCR, ligase chain reaction (LCR), digital PCR,methylation specific-PCR (MSP), co-amplification at lower denaturationtemperature-PCR (COLD-PCR), allele-specific PCR, intersequence-specificPCR (ISS-PCR), whole genome amplification (WGA), inverse PCR, thermalasymmetric interlaced PCR (TAIL-PCR), or other methods includingisothermal amplification methods. Isothermal amplification is a form ofnucleic acid amplification which does not rely on the thermaldenaturation of the target nucleic acid during the amplificationreaction and hence may not require multiple rapid changes intemperature. Isothermal nucleic acid amplification methods can thereforebe carried out inside or outside of a laboratory environment. A numberof isothermal nucleic acid amplification methods have been developed,including but not limited to Strand Displacement Amplification (SDA),Transcription Mediated Amplification (TMA), Nucleic Acid Sequence BasedAmplification (NASBA), Recombinase Polymerase Amplification (RPA),Rolling Circle Amplification (RCA), Ramification Amplification (RAM),Helicase-Dependent Isothermal DNA Amplification (HDA), CircularHelicase-Dependent Amplification (cHDA), Loop-Mediated IsothermalAmplification (LAMP), Single Primer Isothermal Amplification (SPIA),Signal Mediated Amplification of RNA Technology (SMART), Self-SustainedSequence Replication (3 SR), Genome Exponential Amplification Reaction(GEAR) and Isothermal Multiple Displacement Amplification (IMDA).Further examples of such amplification chemistries are described in, forexample, (“Isothermal nucleic acid amplification technologies forpoint-of-care diagnostics: a critical review, Pascal Craw and WamadevaBalachandrana Lab Chip, 2012, 12, 2469-2486, DOI: 10.1039/C2LC40100B,”)incorporated here in its entirety by reference. Isothermal amplificationmethods that operate at temperatures lower than PCR operatingtemperatures can be used, e.g., to improve compatibility of restrictionenzymes with the amplification process if the restriction enzyme is notsufficiently stable under typical PCR operating temperatures.Furthermore, detection methods based on both signal amplification andtarget amplification, such as branched-DNA-based detectionmethodologies, can be used in this approach. For example, forbranched-DNA-based detection methodologies, using an enzyme that cancleave the target in a position located between two positions used forbinding of the capture extender and the label extender (e.g., asdescribed in Tsongalis, Branched DNA Technology in MolecularDiagnostics, Am J Clin Pathol 2006; 126: 448-453), can reduce the signalobtained in the assay when a restriction enzyme recognizes and cleavesthe target.

Reverse-transcription loop mediated isothermal amplification (RT-LAMP)can be used for nucleic acid amplification. RT-LAMP can be used in anassay, including qualitative and quantitative assays for nucleic aciddetection, for example as shown in Examples 1-5, Example 8, or Example9. An RT-LAMP assay can comprise detection of nucleic acids (such as HCVRNA) in at least one step, the test comprising at least one nucleic acidprimer set capable of detecting nucleic acids (such as HCV RNA) in a RTLAMP based molecular test. An RT-LAMP assay use a primer set comprising,for instance, one pair of forward (FIP) and reverse (BIP) inner primers,and forward (F3) primer. An RT-LAMP assay can comprise using loopforward (LF) and/or loop back (LB) primers. An RT-LAMP assay cancomprise using reverse (B3) outer primer. An RT-LAMP assay can compriseusing LF primers that do not anneal or anneal weakly to a template, suchas an HCV RNA template, at a temperature range applicable for reversetranscription, such as but not limited to 37-60° C. The temperaturerange can be optimized for the selected reverse transcription. This canbe done, in some cases, by selecting the LF primers annealing place in asecondary structure rich fragment of HCV 5-UTR RNA template, so that thetemplate self-complimentary duplex Tm for this annealing spot is in arange appropriate for RT-LAMP temperatures, (such as 58-67° C.). It mayalso be done, in some cases, by pre-annealing LF primers (before addingthem to one-step RT-LAMP reaction mixture) with their complementarytemplate-annealing inhibiting oligonucleotides (inhibitors), which, inturn, are 3′ end modified to prevent their elongation by DNA polymerase.Such 3′ end modifications of inhibitors may include but are not limitedto Dideoxycytidine (ddC) or Inverted dT. Such an inhibitor may alsocontain some modified bases, which help to increase the Tm of thecomplex with LoopF primers up to temperatures appropriate for RT-LAMP,such as 58-67° C. An RT-LAMP assay can comprise loop forming primerswhere the 5′ ends and/or 3′ ends (both FIP and BIP) are complementary(or matching) to the target HCV secondary structure small and/or largeloops in the 5′ UTR of the HCV genome, such as, for example, to thedomains II-IV loops in the 5′ UTR HCV structures sequences. An RT-LAMPassay can comprise primers wherein Tm of the B2 annealing is higher thanthe Tm of its complementary template fragment secondary structures,including all the base pairing, hairpin and internal loops, budges andstuck pairs communicated in (but not limited to) the published HCV 5′UTRstructure (see, e.g., “Christopher S. Fraser and Jennifer A. Doudna,Structural and mechanistic insights into hepatitis C viral translationinitiation, Nature Reviews Microbiology 2007, 5: 29-38”). In some casesthe net Tm (the temperature at which half of a template is bound by B2)is in a range applicable for reverse transcription with the used enzyme,including but not limited to 37-63° C. An RT-LAMP assay can compriseprimers wherein the Tm of the B3 annealing is higher than the Tm of itscomplementary template fragment secondary structures for self-assembly,including all the base pairing, hairpin and internal loops, bulges andstuck pairs communicated in (but not limited to) the published HCV 5′UTRstructure (see, e.g., “Christopher S. Fraser and Jennifer A. Doudna,Structural and mechanistic insights into hepatitis C viral translationinitiation, Nature Reviews Microbiology 2007, 5: 29-38”). The net Tm(the temperature at which half of a template is bound by B3) is in arange applicable for reverse transcription with the used enzyme,including but not limited to 37-63° C. In some cases, an RT-LAMP assaycan maximally decrease the probability of loopF primers annealing to RNAtemplate and their subsequent participation as the primers in reversetranscription. In some cases, the RT primers (B2 part of BIP, B3 ifused) and melting temperatures (TmB2 and TmB3) can be balanced to behigher than the melting temperature (Tm2) of the innate secondarystructures of the corresponding parts of the HCV template, and thetemperature of the reverse transcription step can be raised to be higherthan Tm2 as well. The net Tm of B2 and B3 (if used) heteroduplexes withthe template can be in a range applicable for reverse transcription withthe used reverse transcriptase active enzyme. A reverse transcriptasewhich is still active at the temperature higher than Tm2 (including butnot limited to 50-65° C.) can be used. In a one-step format, to ensure adetection of the majority of RNA templates present in reaction solution,the enzyme used for reverse transcription can have an RNase H activity,or a strong displacement activity. In some cases, the elongating ends ofthe priming sequences of BIP and FIP (which are 5′ ends of B1c and F1celongating as 3′ ends of B1, F1; and 3′ ends of B2 and F2) can becomplementary to the secondary structures free fragments of the templateat a chosen temperature applicable for LAMP, such as including but notlimited to 57° C.-72° C.; as an example: the elongating ends of theloop's forming primers (both FIP and BIP in a LAMP reaction) can beplaced to be complementary to the published HCV secondary structures'small or large loops in the 5′ UTR of the HCV genome, such as, forexample, to the domains II-IV loops in the 5′ UTR HCV structuressequences.

Nucleic acid sequence based amplification (NASBA) can be used fornucleic acid amplification. If NASBA is used in combination withrestriction enzymes, the restriction site can be between the forward andreverse primer, including the priming region. This approach is notnecessarily limited to targeting a single restriction site. Multiplerestriction sites on the same target nucleic acid can be targeted,either with one enzyme or with a mixture of several enzymes. Suchmultiple targeting can be used to enhance degradation of the targetmolecules. Such multiple targeting can be used to target multiplevariants of the target molecule that might be present in the mixturebeing analyzed, when, for example, these multiple variants do not needto be differentiated in that analysis. In some cases, reactions can beperformed on the 5′ untranslated region (UTR) of the Hepatitis C Virus(HCV). This region is known to be highly conserved among genotypes ofthe virus, allowing the development of a single amplification reactionthat amplifies, for example, a sequence of 230 basepairs in this region.In some examples, the sequences used for these reactions include, e.g.,the universal forward primer (P1)

(Seq ID No: 1) 5′- AATTCTAATACGACTCACTATAGGG CAAGCACCCTATCAGGCAG TA-3′,the universal reverse primer (P2):5′-GTCTAGCCATGGCGTTAGTA-3′ (Seq ID No:2), or the universal molecular beacon:5′-/FAM/CGATCGAGCCATAGTGGTCTGCGGAACCGGTCGATCG/BHQ1/−3′ (Seq ID No: 3)(DNA or RNA). In some cases, the oligonucleotide modulator specific forHCV Genotype 1 is GT1_antisense: 5′-AATCTCCAGGCAGTGtcgcc-3′ (Seq ID No:4), while the modulator specific for HCV Genotype 2 is GT2_antisense:5′-GACCGGACATAGAGTaaatt-3′ (Seq ID No: 5). The modulators can act toreduce and or inhibit amplification of the target. In this example, theT7 promoter sequence that is part of primer P1 is shown in italics andunderlined and the stem sequence of the molecular beacon is indicated inbold. A universal set of primers can be designed to detect multiple orall HCV genotypes. A pre-incubation step (e.g., 2-5 min at 65° C. andcooling 10 min at 41° C.) can be included in NASBA protocols. The assaycan lack pre-incubation. A NASBA enzyme mix can be made withthermostable enzymes, for example thermostable reverse transcriptase(e.g. RocketScript which may be purchased from Bioneer or MonsterScriptfrom Epicentre), thermostable RNAse H (e.g. Hybridase Thermostable RnaseH which may be purchased from Epicentre or thermostable RNase H2 fromIDT) and thermostable T7 RNA polymerase (e.g. Thermo T7 RNA polymerasewhich may be purchased from Toyobo). The optimum reaction temperature ofthese enzymes is around 50° C.—in some cases the reaction can be run atabout 50° C. to improve the selectivity of annealing of primers (P1 andP2), molecular beacon (DNA or RNA) and specific oligonucleotidemodulators (sense and antisense), and to decrease the free energy ofsecondary structures (kcal/mol).

Nucleic acid-based logic gates and DNA circuits can be used for nucleicacid amplification. The use of restriction enzymes with nucleicacid-based logic gates and DNA circuits can reduce or stop the intrinsicleakage problem for DNA networks. Combining the molecular recognitionability of both restriction enzymes and DNA networks, restriction enzymelogic gates can be highly active components for the design andconstruction of biocomputational devices (e.g., Qian and Winfree,Scaling Up Digital Circuit Computation with DNA Strand DisplacementCascades, Science 2011; 6034: 1196-1201).

Modulators

Modulators (e.g. inhibitors or promoters) can be used in conjunctionwith the methods disclosed herein. Modulators can comprise, for example,restriction enzymes, oligonucleotides, ligase enzymes, engineered ornon-natural nucleases, nucleic acid modifying enzymes, artificialnucleic acids or nucleic acid analogs, modified bases, unnatural bases,or repair proteins. Modulators can be used to recognize specificsequences and slow or stop amplification reactions from occurring. Insome examples, a restriction enzyme can be selected to cleave a sequencelocated between amplification primers, inhibiting amplification. In somecases, an oligonucleotide can be selected to interfere with or blockprimer binding, inhibiting amplification. Modulators can requireactivation; for example, a modulator can be inactive until activated byan enzyme. In one example, an oligonucleotide modulator is incapable orless capable of binding to the target nucleic acid until it isactivated, such as by restriction enzyme digestion or ligase assembly.

Modulators can affect processes in different ways. A modulator candecrease or increase the rate of a reaction. In one example, arestriction enzyme can digest template or amplified nucleic acidmolecules, slowing down an amplification reaction (e.g., reducing therate of production of amplicons). In another example, a restrictionenzyme can affect the structure of a nucleic acid molecule, allowingeasier access to the amplicon and speeding up an amplification reaction(e.g., increasing the rate of production of amplicons). A modulator candecrease or increase the probability or chance that a given moleculewill react, or will react sufficiently to be detected. For example, arestriction enzyme can digest a template nucleic acid molecule,preventing it from being amplified. A modulator can affect theefficiency of a reaction. Modulators can act by competing with thereaction or other process which they modulate. In one example, arestriction enzyme modulator can compete with an amplification reactionfor the template nucleic acid molecule. In another example, anoligonucleotide can compete with nucleic acid amplification primers tobind to the nucleic acid molecule. Modulators can act prior to theprocess which they modulate. Modulators can act during the process whichthey modulate. Modulators can act after the process which they modulate.

Modulators can act on a nucleic acid molecule inside the priming regionof a nucleic acid amplification (within, for example, a margin of onebase). Modulators can act on a nucleic acid molecule outside the primingregion of a nucleic acid amplification (within, for example, a margin ofone base). Modulators can act on a nucleic acid molecule inside theamplicon region of a nucleic acid amplification (within, for example, amargin of one base). Modulators can act on a nucleic acid moleculeoutside the amplicon region of a nucleic acid amplification (within, forexample, a margin of one base). Modulators can act by inhibitingoff-target reactions, thereby promoting the primary reaction. Modulatorscan act on a nucleic acid molecule in a sequence-specific manner or in asequence-targeted manner. For example, a restriction enzyme canrecognize or target a specific sequence or range of sequences, or anoligonucleotide can selectively bind to a target sequence or range ofsequences. Modulators can act on a nucleic acid in amodification-specific or modification-targeted manner. For example, anenzyme can affect nucleic acids in certain states of modification suchas methylation or glycosylation.

Restriction enzymes can be used as modulators. A restriction enzyme canbe type I, type II, type III, type IV, type V or an artificialrestriction enzyme. A restriction enzyme can have digestion activity fordouble stranded DNA, single stranded DNA, or DNA:RNA hybrid molecules. Arestriction enzyme can be thermally stable or not thermally stable.Restriction enzymes compatible with higher-temperature amplification anddetection processes can be selected from those present in thermophilicorganisms, or restriction enzymes with improved stability can beselected from those developed using in vitro selection and in vitroevolution processes. As of October 2013, the Restriction Enzyme Database(REBASE, New England BioLabs) contained over 3800 biochemicallycharacterized restriction enzymes. Of over 3600 Type II REs, over 580are commercially available, including over 220 distinct specificitiesfrom a total of over 250 total specificities known. The availability ofrestriction enzymes allows a wide range of sequences to be targeted as arestriction site.

In some cases, the restriction site can be selected to be locatedbetween the primer sequences used for amplification. It can be selectedto exert an improved or optimized inhibitory effect on the amplificationreaction. For example, when LAMP is used for amplification, therestriction site can be between the B3 primer and the F3 primer (e.g.,see Example 1). In another example, when RPA is used, the restrictionsite can be between the forward primer and the reverse primer, includingthe priming region. In another example, when NASBA is used, therestriction site can be between the forward and reverse primer,including the priming region. This approach is not limited to targetinga single restriction site. Multiple restriction sites on the same targetnucleic acid can be targeted, either with one enzyme or with a mixtureof several enzymes. Such multiple targeting can be used to enhancedegradation of the target molecules, or to target multiple variants ofthe target molecule that might be present in the mixture being analyzed,if, for example, these multiple variants do not need to bedifferentiated in that analysis.

In some cases, the restriction enzyme can also be used outside thepriming region. For example, a restriction enzyme can be used todissociate the secondary structure of RNA and promote the amplificationprocess. In such cases, restriction enzyme activity can be used topromote amplification and detection reactions. Methods, devices, andapproaches discussed herein are not limited to inhibiting or stoppingreactions, but can also be used to promote amplification and detectionreactions. For example, a restriction enzyme digestion can beincorporated into a NASBA reaction to digest out of the amplicon(off-target) regions or products, decreasing the amount of non-specificproduct and enhancing the reaction. Restriction enzymes with a targetsequence not included in the amplified product can be used to omit therecommended pre-incubation step for NASBA.

Artificial restriction enzymes such as zinc-finger nucleases (ZFNs)(see, e.g., “F. D. Urnov, J. C. Miller, Y. L. Lee, C. M. Beausejour, J.M. Rock, S. Augustus, A. C. Jamieson, M. H. Porteus, P. D. Gregory andM. C. Holmes, Highly efficient endogenous human gene correction suingdesigned zinc-finger nucleases, Nature, 2005, 435, 646-51”),transcription activator-like effector nucleases (TALENs) (see, e.g., “M.Christian, T. Cermak, E. L. Doyle, C. Schmidt, F. Zhang, A. Hummel, A.J. Bogdanove and D. F. Voytas, Targeting DNA double-strand breaks withTAL effector nucleases, Genetics, 2010, 186, 757-61”), meganucleases(see, e.g., “G. Silva, L. Poirot, R. Galetto, J. Smith, G. Montoya, P.Duchateau and F. Paques, Meganucleases and other tools for targetedgenome engineering: perspectives and challenges for gene therapy, CurrGene Ther, 2011, 11: 11-27”), or RNA-guided engineered nucleases viaCas9 (RGENs) (see, e.g., P. Mali, L. Yang, K. M. Esvelt, J. Aach, M.Guell, J. E. DiCarlo, J. E. Norville and G. M. Church, RNA-guided humangenome engineering via Cas9, Science, 2013, 339: 823-6 and J. M. Kim, D.Kim, S. Kim” and “J. S. Kim, Genotyping with CRISPR-Cas-derivedRNA-guided endonucleases, Nat Commun, 2014, 5, 3157”) can be used totarget identified genetic markers.

At least three types (I-III) of clustered short palindromic repeats(CRISPR) systems have been identified across a wide range of bacterialhosts and can be used as modulators. Type I and III systems use aspecialized CRISPR-associated nuclease (Cas) that processes theprecursor CRISPR RNA (pre-crRNA), and once mature, each crRNA assemblesinto a large multi-Cas protein complex capable of recognizing andcleaving nucleic acids complementary to the crRNA. In contrast, type IICRISPR process pre-crRNAs by a different mechanism in which atrans-activating crRNA (tracrRNA) complementary to the repeat sequencesin pre-crRNA triggers processing by the double double-stranded (ds)RNA-specific ribonuclease RNase II in the presence of Cas9 protein.Following the hybridization between the two non-coding RNAs, Cas9 istargeted to the genomic loci matching a 20 nucleotide guide within thecrRNA, immediately upstream of a 5′NGG protospacer adjacent motif (PAM).crRNA and tracrRNA can be fused to generate a chimeric single-guide RNA(sgRNA) that mimics the natural crRNA-tracrRNA hybrid. BothcrRNA-tracrRNA duplexes and sgRNA can be used to target Cas9 formultiplexed genome editing. The methodologies described herein caninclude the use of the CRISPR system to affect the processes ofdetection or amplification. Methodologies can include the use of Cas9 orits homologues or functional analogues, such as crRNA and tracrRNA orsgRNA (origin of RNA includes the one made in situ or ex situ by invitro transcription) to control nucleic acid amplification processes ina sequence specific manner, where the activity of Cas9 can be preservedor partially preserved under the conditions of amplification ordetection. In some examples, the specificity of the Cas9-crRNA-tracrRNAor Cas9-sgRNA complexes can be modified by matching the sequence of thecrRNA with the target of interest. In some examples, these elementscould be combined with a detection or an amplification scheme toidentify, detect or differentiate nucleic acid sequences. In someexamples, by mixing these three elements in a PCR reaction, togetherwith the DNA or RNA template, the PCR product can be cleaved whileamplification is occurring, changing the outcome of the reaction (e.g.,including but not limited to: from positive to negative, delayed time topositive or less number of counts in digital format) and avoidingadditional steps which other methods, such as RFLP, can entail. Thiscleavage can occur, for example, based on a specific single nucleotidepolymorphism (SNP) and the sequence surrounding it. Isothermalamplification methods (e.g., NASBA, LAMP, RPA, RCA) can have highcompatibility with Cas9 systems during the process of amplification andcan be used. In some examples, the use of engineered Cas9-crRNA-tracrRNAcan overcome the limited availability of restriction endonuclease sites.

Ligase enzymes can be used as modulators, including as inhibitors orpromoters. For example, a ligase enzyme can ligate two nucleic acidmolecules, allowing subsequent amplification of the ligated product. Aligase enzyme can ligate two nucleic acid molecules, promoting a foldingof the ligated product with inhibits, prevents, promotes, or enablessubsequent amplification.

Oligonucleotides can be used as modulators, including as inhibitors(“oligos” or “oligo inhibitors”). Recognition, hybridization andblocking of a specific sequence by an oligonucleotide can be used tostop or delay a reaction of interest. The use of oligonucleotides is notlimited to inhibition of reactions, and can also be used to enhancecertain reactions, for example by affecting the secondary structure of anucleotide target, or by inhibiting off-target reactions.Oligonucleotides can comprise synthetic or naturally produced nucleicacid molecules. Modified nucleic acids or nucleic-acid-like structures(e.g., peptide nucleic acids or PNAs) can also be used, which can alsobe referred to as “oligos” or “oligo inhibitors.” In some examples, anoligonucleotide inhibitor binds more tightly or faster to the targettemplate or intermediate product than, for example, the primers in theamplification reaction. These oligonucleotides can be longer thanprimers used for amplification. These oligonucleotides can contain baseswith or without modifications that bind more tightly to the target.These oligonucleotides can be designed with special structures (e.g.,toe-hold structures), such as those used to facilitate, accelerate orimprove the specificity of DNA origami, DNA self-assembly, or DNAcircuits. The specificity of inhibitors can be controlled or altered, insome examples, by the sequence of the oligonucleotides, which can betuned by a number of methods, including by altering the percentage ofmatches between inhibitors and template, or primers and template. Theoligonucleotides can, in some cases, include some modifications (e.g.,locked nucleic acid (LNA) or dideoxynucleotides (ddNTPs)), to increasethe specificity, change the annealing temperature, or produce a strongerinhibition effect. If the priming region is targeted, theoligonucleotide inhibitor can be chosen to bind more tightly or fasterto the target template or intermediate product (for example, it belonger than primers used for amplification, or contain bases with orwithout modifications that bind more tightly to the target) than theprimers in the competition. The specificity of the inhibitors can becontrolled by the sequence of the oligonucleotide, which can be tuned bya number of methods, including by altering the percentage of matchesbetween inhibitors and template, or primers and template. Theoligonucleotides could include some modifications (e.g., LNA, ddNTPs) toincrease the specificity, change the annealing temperature, or produce astronger inhibition effect.

Oligonucleotides can comprise peptide nucleic acid (PNA). Peptidenucleic acid is a type of nucleic acid analogue that replaces the sugarphosphate backbone with N-(2-amino-ethyl)-glycine units. Due to the factthat the backbone is uncharged, unlike DNA, the thermal stability of aPNA:DNA duplex is higher than that of dsDNA. It is also resistant tohydrolytic (enzymatic) cleavage and typically cannot be recognized bypolymerase as a primer from which to extend. PNA-directed PCR clampingand selective inhibition by PNA in an isothermal amplification systemcan be used with the methodologies described herein. The followingpublications are incorporated here by reference in their entireties forall purposes: “Drum, H., P. E. Nielsen, M. Egholm, R. H. Berg, O.Buchardt, and C. Stanley, Single base pair mutation analysis by PNAdirected PCR clamping, Nucleic Acids Res 1993, 21(23): 5332-5336,” “KTatsumi, Y Mitani, J Watanabe, H Takakura, K Hoshi, Y Kawai, T Kikuchi,Y Kogo, A Oguchi-Katayama, Y Tomaru, H Kanamori, M Baba, T I shadao, KUsui, M Itoh, P E Cizdziel, A Lezhava, M Ueda, Y Ichikawa, I Endo, STogo, H Shimada, and Y Hayashizaki, Rapid screening assay for KRASmutations by the modified smart amplification process, J Mol Diagn 2008,10(6): 520-526,” “Jae-jin Choi, Chunhee Kim, and Heekyung Park, Peptidenucleic acid-based array for detecting and genotyping humanpapillomaviruses. J Clin Microbiol 2009, 47(6): 1785-1790,” and“Lizardi, P. M. (1993) Rolling circle replication reporter systems, YaleUniversity, U.S. Pat. No. 7,618,776 B2.” Together with some nucleases(e.g., 51 nuclease), PNA can function as an artificial restrictionenzyme by the invasion mechanism to dsDNA of PNA and degradation bynuclease of the generated ssDNA part, (see, e.g., “A. Ray and B. Norden,Peptide nucleic acid (PNA): its medical and biotechnical applicationsand promise for the future, FASEB J 2000, 14: 1041-1060”). In someexamples, this approach can be used in combination with one or moreisothermal amplification chemistry. This approach can be used with avariety of target nucleic acids (ssDNA, RNA, dsRNA or dsDNA). Using PNAas a diagnostic tool for genotyping and subtyping (e.g., of influenza)can be conducted qualitatively or quantitatively. The materials andmethods described in (“K Kaihatsu, S Sawada, and N Kato, RapidIdentification of Swine-Origin Influenza A Virus by Peptide Nucleic AcidChromatography, Antivirals & Antiretrovirals 2013, 5(4): 077-079”) canbe used in combination with the methodologies described herein.

Oligonucleotides (e.g., unmodified oligonucleotides such as RNA and DNA,and modified oligonucleotides such as PNA and LNA) can be used alone orin combination with certain enzymes (e.g., genome editing engineerednucleases or methylase) as modulators, to tune the process ofamplification in a sequence-specific manner. This can allow targetingnew emerging targets while retaining the assay setup, and the highthroughput in screening different sequences, which could facilitatepandemic disease monitoring and epidemiological surveillance, forexample in the case of influenza A genotyping/subtyping.

Oligonucleotide modulators can be used in combination with RNase H tomodulate a nucleic acid amplification reaction. For example, asequence-specific DNA oligonucleotide modulator (e.g., an inhibitor)complementary to an RNA template or product RNA (e.g., antisense RNAproduced by NASBA reaction), can anneal to a target nucleic acid andgenerate a DNA/RNA hybrid recognizable by RNase H. RNase H can be usedto cleave the RNA strand from a heteroduplex. This oligonucleotidemodulator-guided cleavage can prevent further amplification of the RNAstrand, changing rate of the reaction or final number of amplifiedmolecules (“fate”). The guide-RNase H can be used to target specificsequences within a sequence targeted by a variety amplificationreactions, including but not limited to Recombinase PolymeraseAmplification (RPA), Loop-mediated isothermal amplification (LAMP),Helicase-dependent amplification (HAD), Strand displacementamplification (SDA), and Nicking enzyme amplification reaction (NEAR).

RNA molecular beacons can be used as modulators. For example, an RNAmolecular beacon and an increased concentration of RNase H can be usedto increase the efficiency of a NASBA reaction. NASBA makes use of RNaseH to degrade the RNA/DNA heteroduplex created by reverse transcription,enabling the hybridization of additional primers and the generation ofdouble-stranded DNA. Therefore, higher RNase H concentration can benefitthe performance of NASBA reaction because the described steps willproceed more rapidly. The amount of RNase H can be limited because ofthe presence of sequence specific DNA molecular beacons, which canhybridize to a NASBA product (e.g. antisense RNA) generating a DNA/RNAheteroduplex that can be recognized and cleaved by the RNase H. At highconcentration this cleavage of the NASBA product decreases theefficiency of the reaction. In order to increase efficiency of NASBAreaction while avoiding undesired cleavage an RNA molecular beacon canbe used, allowing an increased amount of RNase H. A thermostable RNase Hcan be used, e.g, to avoid losing activity during steps with elevatedtemperature (e.g. pre-incubation of NASBA reaction). The binding ofprimers to RNA templates can produce a DNA/RNA heteroduplex detectableby RNase H. In some examples, this modified NASBA reaction can make useof RNA-containing primers P1 or P2 to prevent the RNase H mediateddegradation of template due to primer annealing. A modulator can be anon-specific nuclease that cleaves RNA.

The enzyme RNase H is a non-specific nuclease that cleaves RNA. RNaseH's ribonuclease activity cleaves the 3′-O—P bond of RNA in a DNA/RNAduplex to produce 3′-hydroxyl and 5-phosphate terminated products.Therefore, RNAse H can be used as a modulator of an amplificationreaction by cleaving the RNA template or by cleaving the generated RNAproduct (e.g., in a NASBA reaction). Other RNA- and DNA-cleaving enzymescan be used as well. FIG. 4 shows an exemplary schematic of a NASBAamplification reaction with the P1 (antisense)-P2 (sense) primer set.The overhang on the P1 encodes the promoter sequence for the T7 RNApolymerase. A molecular beacon with a fluorophore and a quencher withthe NASBA amplification reaction can generate a real-time detectionsystem. Antisense oligonucleotide (AO) modulator guides RNase H tospecifically cleave RNA template while sense oligonucleotide (SO)modulator guides RNase H to specifically cleave generated antisense RNA.Antisense oligonucleotide (AO) modulator and sense oligonucleotide (SO)modulator can be used individually or in combination. DNA or RNAmolecular beacons target antisense RNA In some cases, in order tomodulate the reaction in a sequence specific manner, the amplificationsystem can be modified by the incorporation of RNAse H and anoligonucleotide modulator complementary to the targeted RNA. In someexamples, this oligonucleotide can anneal to the target RNA strand, andin some examples it can generate a DNA/RNA hybrid that will berecognized by the RNAse H, cleaving the RNA template and consequentlyreducing the initial amount of template that would proceed to asuccessful amplification (Antisense Oligonucleotide (AO), FIG. 4). Insome cases, the oligonucleotide modulator can target the produced RNA(e.g., antisense RNA) and can slow down the reaction (SenseOligonucleotide (SO), FIG. 4). In some examples, the combination of aspecific oligonucleotide modulator together with a non-specific nucleasecan generate a guide-RNase H that can be used to specifically target asequence of interest. In order to cleave the RNA, RNAse H needs aDNA/RNA hybrid with 4 or more nucleotides perfectly matched (see, e.g.,“Donis-Keller H. Site specific enzymatic cleavage of RNA. Nucleic AcidsRes. 1979 Sep. 11; 7(1):179-92”). This property can be used to identifysingle nucleotide point mutations. For example, in some cases anoligonucleotide modulator of 7 bases can be designed to target asequence where a SNP (single nucleotide polymorphism) could be presentin the 4th position; the oligonucleotide can hybridize under correctreaction conditions in the presence or absence of the SNP, but RNAse Hactivity can be limited due to the absence of the SNP. A perfectlymatching RNA/DNA hybrid can be cleaved, preventing amplification of thetemplate, while the presence of a SNP can prevent RNAse H activity,allowing amplification as normal. Other enzymes that are sensitive tomatched or mismatched hybridization products can be used similarly,including enzymes that detect one or more modifications of one or moreof nucleic acid bases. The units of RNase H typical NASBA reactions canbe limited because readout can be tied to the presence of specific DNAmolecular beacons (oligonucleotide hybridization probes that can reportthe presence of specific nucleic acid) which hybridize to the majorNASBA product, antisense RNA, generating a DNA/RNA heteroduplex. In suchcases, at high concentrations, RNase H can cleave the RNA and theefficiency of the reaction can be reduced. Increasing the amount ofRNAse H can benefit the performance of the reaction because steps inwhich RNAse H is involved (indicated with an asterisk, FIG. 4) willproceed more rapidly; however this can be balanced with the cleavageinduced by the presence of DNA molecular beacon. In some examples, inorder to increase RNAseH concentration and positively affect efficiencyof guided-RNAse H, the NASBA reaction can be modified in one or more ofthe following ways: (i) increase the amount of RNase H; (ii), select athermostable RNAseH to avoid losing activity during pre-incubation ofNASBA reaction; (iii) incorporate an RNA molecular beacon to avoidundesired cleavage promoted by the DNA probe/RNA antisense hybrid. As aresult of this change to an RNA beacon, in modified NASBA, reactionefficiency can be improved. In addition, the competition between theconcentrations of molecular beacons in the system with the RNAse Hactivity can be reduced or eliminated. As a result, greater quantitiesof the RNA based molecular beacon can be added to increase thefluorescent intensity of the product. In another example, theGuide-RNase H system can be used to increase the specificity or accuracyof amplification reactions. By incorporating oligonucleotides thatcannot hybridize to the target sequence for amplification, but rather tooff-target NASBA products, these side-reactions can be selectivelyinhibited. In addition, it is possible to generate oligonucleotides thatdiffer from conserved template regions by enough bases to preventannealing at reaction temperatures. The activity of RNase H can thenprevent the accumulation of errors in these regions. For example: NASBAis known to suffer from the amplification of off-target sequences due toits use of error-prone T7 polymerase and AMV reverse transcriptase. As aresult, off-target oligonucleotides can be targeted this way to theregion of a molecular beacon thus preventing the amplification ofproducts undetectable by the beacon. In another example, this inhibitionof non-specific product can be caused not by the use of the Guide-RNaseH system but rather by the use of restriction enzymes. In one example,the restriction enzyme ApoI was shown to recover the specificity of aNASBA reaction performed without a pre-incubation step.

Repair proteins (e.g., MutH, MutL, and MutS) can be used to produce asequence specific interference or inhibition of a nucleic acidamplification system: For example, the Escherichia coli methyl-directedDNA mismatch repair system (see, e.g., “Smith, J. and P. Modrich,Mutation detection with MutH, MutL, and MutS mismatch repair proteins.Proc Natl Acad Sci USA 1996, 93(9): 4374-4379”) can identify and repairbase-base mispairs and up to three nucleotide insertion/deletionmismatches. Repair is initiated by binding of MutS to the mispair.Binding of MutL to this complex results in activation of MutH(ATP-dependent activation of endonuclease activity), which incises theheteroduplex at d(GATC) sequences in the vicinity of the mispair. Insome examples, combining the complex MutHLS or using one of these threeproteins together with a nucleic acid amplification system can producesequence-specific interference of the system. MutS is able to suppress anucleic acid extension reaction by binding specifically to a mismatchedbase pair (see, e.g., Hayashizaki, Y; Itoh, M.; Usui K.; Kazuhito M.;and Kanamori H., Novel MutS protein and method of using same todetermine mutations, 2011, Patent number EP 2 371 951 A1). This approachis not limited to these specific proteins; rather, other proteins withrelated functional activities can be used instead or in addition tothese proteins.

Chemical modification of nucleic acids can be used to modulate nucleicacid amplification. For example, a DNA intercalator modified with anazide group (e.g., propidium monoazide (PMA)) or other cross-linkinggroup can be used as a modulator, inducing modification of DNA that caninterfere with amplification or detection reactions. Providing both achemical modifier and reagents for amplification or detection reactionscan allow competition between the modification reaction and theamplification or detection reaction. Chemically modified probes (e.g.,oligonucleotides, PMA, or other probes described herein), similarlymodified with azide or other cross-linking groups, can providespecificity in associating with a target nucleic acid and modulating(e.g., inhibiting) amplification or detection reactions. Similarly,these approaches can be used to enhance association between a primer anda target nucleic acid, promoting amplification.

Assays

The devices and methods described herein can be applied for assays todetect genetic variation, including differences in genotypes, ranging insize from a single nucleotide site to large nucleotide sequences visibleat a chromosomal level. Such genotype or polymorphism analysis can beused for applications including but not limited to early diagnosis,prevention and treatment of human diseases; systematics and taxonomy;population, quantitative, and evolutionary genetics; plant and animalbreeding; identifying individuals and populations (paternity andforensic analysis), infectious disease diagnostics and monitoring andsurveillance, epidemiology. Examples of some applications of inventionsdescribed herein are provided herein. These applications are not limitedto the use of any of the methods described herein may be used for theseapplications, including those using different modulators (e.g.,restriction enzymes or oligonucleotides), including inhibitors orpromoters.

An assay can comprise conducting a reaction (e.g., amplification) on areagent (e.g., nucleic acid) in the presence of a modulator (e.g.,restriction enzyme) and comparing the results of the reaction (e.g.,reaction rate, reaction efficiency, reaction outcome, positive ornegative signal generation) to a reaction conducted without a modulator.This can reveal a difference in reaction outcome, indicating thepresence or identity of a reagent which is affected by the chosenmodulator. An assay can comprise conducting a reaction (e.g.,amplification) on a reagent (e.g., nucleic acid) in the presence of amodulator (e.g., restriction enzyme) and comparing the results of thereaction (e.g., reaction rate, reaction efficiency, reaction outcome,positive or negative signal generation) to a reaction conducted on adifferent reagent. This can reveal a difference in the effect of themodulator on the two different reagents, indicating the identity of thereagents or of the modulator. An assay can comprise conducting multiplereactions (e.g., amplification) on a reagent (e.g., nucleic acid) in thepresence or absence of a modulator (e.g., restriction enzyme) ormultiple modulators; the pattern of reaction outcomes in the presence orabsence of each modulator can be used to generate a pattern or“fingerprint.” This pattern can be compared to one or more referencepatterns indicating a particular reagent (e.g., a nucleic acid with aparticular genotype), allowing identification of the reagent. Modulatorscan be provided before, during, or after various sample handling steps,sample preparation steps, or reaction steps. The above assays can beextended to 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more different reagents,modulators, or both.

Modulators (e.g., restriction enzymes or oligonucleotides), eitherpromoters or inhibitors, can be used in conducting multiplexedmeasurements. For example, when multiple variants (e.g., genotypes ofthe HCV virus) need to be differentiated, multiple restriction enzymescan be chosen to selectively target amplicons arising from thesegenotypes. These reactions can be, for example, performed in separatecompartments for each enzyme or enzyme mixture, as described elsewherein this application for multiplexed measurements. A sufficient number ofrestriction enzymes of sufficiently different selectivity can be chosensuch that each variant can be uniquely identified. For example, thenumber of enzymes used can be equal to or larger than the number ofvariants to be differentiated and identified, although this is notalways required. In some examples, a cascade that processes samplessequentially through several conditions can be applied to provide higherthroughput. One reaction can run through multiple steps for short amountof time, and then the reaction result can be read out only at the laststep of the cascade, or the result for all steps can be read out at onceat the end of the cascade. The restriction enzyme can be deactivated atthe end of each step of the cascade. The system can be designed in a way(e.g., by using different primers for each condition) that only when thetarget is specific to a certain combination of enzymes is a positivereadout generated in the last step. Thus the spatial multiplexing ofrestriction enzymes, such as in FIG. 3, can be transferred to temporalmultiplexing. FIG. 3 shows exemplary nucleic acid profiling panels. FIG.3A shows one set of universal primers or amplification chemistry withdifferent restriction enzymes in each compartment. FIG. 3B shows onetype of restriction enzyme with different sets of primers oramplification chemistries in each compartment. FIG. 3C shows multiplesets of primers or amplification chemistries with multiple restrictionenzymes. FIG. 3D shows each compartment further divided into smallercompartments to perform digital amplification or detection, where onesmaller compartment only contains one molecule or no molecule. Whitespots represent positive reactions (e.g., the restriction enzyme doesnot substantially recognize any target sequence and does notsignificantly influence the reaction rate), while the black spotsrepresent negative reactions (e.g., the restriction enzyme recognizes atarget sequence in the amplicon and so the reaction is delayed orstopped). Each species or genotype assayed can generate a specificnucleic profile or “fingerprint” corresponding to its identity. Thisexemplary assay can also be implemented using other modulators, such asoligonucleotides. This highly multiplexed panel can be performed in anyformat comprising confined volumes, for example, on a well plate, in aSlipChip device (e.g., Feng Shen, Wenbin Du, Elena K. Davydova, MikhailA. Karymov, Janmaj ay Pandey, and Rustem F. Ismagilov, NanoliterMultiplex PCR Arrays on a SlipChip, Analytical Chemistry 2010;82:4606-4612), in an emulsion droplet system (e.g., RainDance orQuantalife systems), or functionalized bead (e.g., BeadArray or Luminexsystems).

Assays can comprise genetic fingerprinting (e.g., DNA testing, DNAtyping or DNA profiling). This methodology can use the individuality ofDNA molecules to distinguish between organisms or to show therelationships between them. For example, restriction fragment lengthpolymorphism (RFLP) analysis can be used for genetic fingerprinting.Detecting RFLPs involves fragmenting a sample of DNA by a restrictionenzyme, which can recognize and cut DNA wherever a specific shortsequence occurs. The resulting DNA fragments can then be separated bylength, for example through an agarose gel electrophoresis, andanalyzed, for example by transfer to a membrane via the Southern blotprocedure followed by hybridization of the membrane to a labeled DNAprobe to determine the length of the fragments which are complementaryto the probe. An RFLP occurs when the length of a detected fragmentvaries between individuals and can be used in genetic analysis. Assaysdisclosed herein can produce a distinct pattern based on the generationof a specific amplicon and the combination of different restrictionenzymes during the amplification method, for example as shown in FIG. 3.This methodology does not require post-amplification treatment for thereadout and can generate a specific identity or fingerprint for eachanalyzed target. Using a panel comprising one or more preloadedrestriction enzymes can be used to generate a DNA profile for a specificamplicon or amplicons. Exemplary applications of this assay includeepidemiological surveillance (for example, microbiological typingsystems for Salmonella spp., Escherichia spp., Staphylococcus spp.,Campylobacter spp., Listeria spp. and others); bacterial species aregrouped showing maximal similarity phenotypic and genotypic characters,however species may often be subdivided (“typed”) on the basis ofcharacters of a single class (e.g., biotyping, serotyping, phage typing,bacteriocin typing) and practical use of this can be made to obtaininformation about sources and routes of infection (epidemiologicalsurveillance). Other applications include characterization of geneticpatterns associated to health or diseases status (e.g., cancer),detection of drug resistance mutations (e.g., HIV and HCV), andidentification of antibiotic resistance (e.g., Methicillin-resistantStaphylococcus aureus (MRSA)) can be accomplished using themethodologies described herein.

An assay can comprise conducting one or more reactions on a target andobserving reaction results. For example, an assay can comprise combiningreagents for two different reactions with a target shared by bothreactions, and observing the outcome of the competing reactions. Theoutcome can be observed and used to determine information about one ormore of the conducted reactions, such as reaction rate or reactionefficiency.

Assays can be conducted in a digital format, that is, assays can beconducted on a sample divided into partitions containing one or zerotarget molecules (e.g., nucleic acid molecules). In some cases, somepartitions can contain more than one target molecule; in some cases, themajority of partitions contain one or zero target molecules. Thisdigital or single molecule format can be used in conjunction with assaysdescribed herein, including identification, detection, genotyping, SNPdetection, rare allele detection, and quantification of nucleic acids.Modulation, including inhibition, of a reaction at single molecule levelcan be different from that at bulk level. For example, in the case ofinhibition by restriction enzyme, in bulk reaction, a molecule that isnot inhibited or is less inhibited can cause amplification or detection,thus lead to a positive of the entire mixture. In a digital singlemolecule format, such a molecule will be confined, for example, to asingle partition or compartment, leading to a positive in that singlecompartment. Results can be presented in a binary format (e.g., yes/no,on/off), with each partition either giving rise to a signal or notgiving rise to a signal (e.g., an indicator or readout reaches or doesnot reach a chosen threshold value). By performing the reaction indigital format, it is possible to translate a kinetic difference inamplification between into probability difference (e.g., an increased ordecreased probability that a single sample molecule present in apartition will be amplified), as shown for example in FIG. 10, allowingthe binary results from the partitions to be read or collected with anend-point measurement. Quantitative results can also be obtained fromdigital assays, allowing both genotyping and quantification of viralload, for example. Quantitative results can also be obtained from asample with more than type of one target nucleic acid present, allowinganalysis of a population distribution between targets. Real-timemonitoring during the reaction can be used, alone or in combination withdigital or binary format results, to observe a kinetic difference inamplification between samples. Real-time digital analysis can provideinformation on the rate of individual amplification reactions, on thedistribution and the heterogeneity of the rate of the amplificationreactions, and on the number of successful amplification reactions. Thisinformation, in combination with the methods and reagents describedherein, can be used to enhance the quality of nucleic acid analysis ordetection. For example, real time digital analysis can be used toanalyze HCV genotyping RT-LAMP reactions. Real-time digital analysis isnot required for all cases, and end-point digital analysis can besufficient. In end-point digital analysis, as described above, a singlemeasurement of the extent of reaction is obtained for the partitions orcompartments of interest, and used for analysis. Assays can also beperformed in a quasi-digital format, which is similar to the digitalformat described above except that more than one copy of a target (e.g.,2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, or morecopies of a target) can be present in a single partition. In some cases,more than one copy of a target can be present in the majority ofpartitions. Nonetheless, each partition either generates a positive or anegative signal, and results can be analyzed similarly to a digitalassay.

Examples of digital amplification and examples of genotypingapplications are described in the following patents and papersincorporated here by reference in their entirety: U.S. Application61/516,628, “Digital Isothermal Quantification of Nucleic Acids ViaSimultaneous Chemical Initiation of Recombinase Polymerase Amplification(RPA) Reactions on Slip Chip,” filed on Apr. 5, 2011; U.S. Application61/518,601, “Quantification of Nucleic Acids With Large Dynamic RangeUsing Multivolume Digital Reverse Transcription PCR (RT-PCR) On ARotational Slip Chip Tested With Viral Load,” filed on May 9, 2011; U.S.application Ser. No. 13/257,811, “Slip Chip Device and Methods,” filedon Sep. 20, 2011; international application PCT/US2010/028361, “SlipChip Device and Methods,” filed on Mar. 23, 2010; U.S. Application61/262,375, “Slip Chip Device and Methods,” filed on Nov. 18, 2009; U.S.Application 61/162,922, “Sip Chip Device and Methods,” filed on Mar. 24,2009; U.S. Application 61/340,872, “Slip Chip Device and Methods,” filedon Mar. 22, 2010; U.S. application Ser. No. 13/440,371, “AnalysisDevices, Kits, And Related Methods For Digital Quantification Of NucleicAcids And Other Analytes,” filed on Apr. 5, 2012; and U.S. applicationSer. No. 13/467,482, “Multivolume Devices, Kits, Related Methods forQuantification and Detection of Nucleic Acids and Other Analytes,” filedon May 9, 2012; U.S. application Ser. No. 13/868,028, “Fluidic Devicesand Systems for Sample Preparation or Autonomous Analysis,” filed onApr. 22, 2013; U.S. application Ser. No. 13/868,009, “Fluidic Devicesfor Biospecimen Preservation,” filed on Apr. 22, 2013; and internationalapplication PCT/US13/63594, “Methods and Systems for MicrofluidicsImaging and Analysis,” filed on Oct. 4, 2013; Feng Shen, Wenbin Du,Jason E. Kreutz, Alice Fok, and Rustem F. Ismagilov, “Digital PCR on aSlipChip,” Lab Chip 2010 10: 2666-2672; Feng Shen, Elena K. Davydova,Wenbin Du, Jason E. Kreutz, Olaf Piepenburg, and Rustem F. Ismagilov,“Digital Isothermal Quantification of Nucleic Acids via SimultaneousChemical Initiation of Recombinase Polymerase Amplification Reactions onSlipChip,” Analytical Chemistry 2011 83:3533-3540; Feng Shen, Bing Sun,Jason E. Kreutz, Elena K. Davydova, Wenbin Du, Poluru L. Reddy, Loren J.Joseph, and Rustem F. Ismagilov, “Multiplexed Quantification of NucleicAcids with Large Dynamic Range Using Multivolume Digital RT-PCR on aRotational SlipChip Tested with HIV and Hepatitis C Viral Load,” JACS2011 133: 17705-17712; Christina Fan, H., Gu, W., Wang, J., Blumenfeld,Y. J., El-Sayed, Y. Y. & Quake, S. R. Non-invasive prenatal measurementof the fetal genome. Nature 487, 320-324, (2012); Gansen, A., Herrick,A. M., Dimov, I. K., Lee, L. P. & Chiu, D. T. Digital LAMP in a sampleself-digitization (SD) chip. Lab Chip 12, 2247-2254, (2012); Thorsen,T., Maerkl, S. J. & Quake, S. R. Microfluidic large-scale integration.Science 298, 580-584, (2002); Ottesen, E. A., Hong, J. W., Quake, S. R.& Leadbetter, J. R. Microfluidic digital PCR enables multigene analysisof individual environmental bacteria. Science 314, 1464-1467, (2006);Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L. & Quake, S. R.Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA frommaternal blood. Proc. Natl. Acad. Sci., U.S.A. 105, 16266-16271, (2008);Du, W. B., Li, L., Nichols, K. P. & Ismagilov, R. F. SlipChip. Lab Chip9, 2286-2292, (2009); Fan, H. C., Blumenfeld, Y. J., El-Sayed, Y. Y.,Chueh, J. & Quake, S. R. Microfluidic digital PCR enables rapid prenataldiagnosis of fetal aneuploidy. Am. J. Ob. Gynecol. 200,543.e541-543.e547, (2009); Liu, W. S., Chen, D. L., Du, W. B., Nichols,K. P. & Ismagilov, R. F. Slip Chip for Immunoassays in NanoliterVolumes. Anal. Chem. 82, 3276-3282, (2010); Shen, F., Du, W. B.,Davydova, E. K., Karymov, M. A., Pandey, J. & Ismagilov, R. F. NanoliterMultiplex PCR Arrays on a SlipChip. Anal. Chem. 82, 4606-4612, (2010);Heyries, K. A., Tropini, C., VanInsberghe, M., Doolin, C., Petriv, O.I., Singhal, A., Leung, K., Hughesman, C. B. & Hansen, C. L. Megapixeldigital PCR. Nat. Methods 8, 649-U664, (2011).

Readouts

Assay results can comprise a readout or detection mechanism chosen froma range of readouts used to detect progress or results of reactions.Examples include but are not limited to electrochemical readouts,optical readouts, including for example fluorescence readouts,colorimetric readouts, chemiluminescence, electrical signals, quenching,probe binding, probe hybridization, metal labeling, contrast agentlabeling, absorbance, mass spectrometry, sequencing, lateral flowstrips, and the generation of a heterogeneous substance (e.g.,precipitation, gas bubble).

A readout mechanism can comprise fluorescence. For example fluorescentdye can be used to label nucleic acids; reactions with more nucleic acidproduct can yield more fluorescence signal. Fluorescent dyes can includebut are not limited to ethidium bromide, berberine, proflavine,daunomycin, doxorubicin, thalidomide, YOYO-1, SYBR Green I, SYBR GreenII, oxazole yellow (YO), thiazole orange (TO), PicoGreen (PG), TOTO,TO-PRO, SYTOX, SYTO, other cyanine dyes, and calcein. The fluorescenceintensity can be measured at an end-point or in real-time, allowingmeasurement of the reaction progress. For example, a given level offluorescence can be set as the threshold for a positive signal from adigital or quasi-digital compartment. Alternatively, a readout mechanismcan operate without fluorescence.

A readout mechanism can comprise mass spectrometry. For example, nucleicacids of different sizes (e.g. from restriction digestion or ligation)can be distinguished and/or counted by mass spectrometry. Alternatively,a readout mechanism can operate without mass spectrometry.

A readout mechanism can comprise electrophoresis, including gelelectrophoresis. For example, nucleic acids of different sizes (e.g.from restriction digestion or ligation) can be identified ordistinguished by electrophoresis. Alternatively, a readout mechanism canoperate without electrophoresis.

A readout mechanism can comprise sequencing. Sequencing, or sequencedetermination techniques, can be performed by methods including but notlimited to Sanger sequencing, Illumina (Solexa) sequencing,pyrosequencing, next generation sequencing, Maxam-Gilbert sequencing,chain termination methods, shotgun sequencing, or bridge PCR; nextgeneration sequencing methodologies can comprise massively parallelsignature sequencing, polony sequencing, SOLiD sequencing, Ion Torrentsemiconductor sequencing, DNA nanoball sequencing, Heliscope singlemolecule sequencing, single molecule real time (SMRT) sequencing,nanopore DNA sequencing, tunnelling currents DNA sequencing, sequencingby hybridization, sequencing with mass spectrometry, microfluidic Sangersequencing, microscopy-based techniques, RNA polymerase sequencing or invitro virus high-throughput sequencing. Sequencing reads can be used toidentify reaction products, and the number of sequencing reads generatedfor a given nucleic acid product can be used to evaluate the reaction.For example, a given number of sequencing reads can be set as thethreshold for a positive signal from a digital or quasi-digitalcompartment. Alternatively, a readout mechanism can operate withoutsequencing.

Signal can be detected by a variety of techniques, including but notlimited to optical techniques, electrical techniques or magnetictechniques. The signal can be optically detectable, for examplefluorescent signal, phosphorescent signal, colorimetric signal,absorption signal, or scattering signal.

In some cases, a modulator can act on the read-out or detectionmechanism. For example, a modulator can affect the generation of afluorescent signal, the conducting of a sequencing reaction, theformation of precipitate, the formation of a gas bubble, or otherread-out or detection mechanisms. For example, a modulator can ligate anucleic acid molecule to prepare it for subsequent detection (e.g.,sequencing or probe hybridization), or a modulator can digest a nucleicacid molecule to prevent subsequent detection (e.g., sequencing or probehybridization). In another example, a modulator can be added to anamplification reaction where a fluorescent probe (e.g., molecularbeacon, TaqMan, or Fluorescence Resonance Energy Transfer (FRET) probe)is employed to generate a specific fluorescent signal. Fluorescentprobes can be designed to hybridize within the amplification product. Insome cases, the addition of a modulator (e.g., an oligonucleotide) thathybridizes on the same target as the probe, or a target similar to thetarget on the probe, can prevent the interaction (e.g., by acting as ablock) between the probe and the amplification product and thus canaffect the readout. Specificity of modulators and probes can bedifferent. In some cases, the modulator can bond to a specific region ofa nucleic acid, such as for example to a SNP, and the modulator canconfer to the probe the ability to discriminate between sequences. Insome cases, probes can be sensitive to the presence of a SNP withouttargeting the specific area where the SNP is located.

In some examples, the methods described here can be used to selectgenomic regions of interest and enrich regions of interest (e.g.,regions of eukaryotic genomes) before sequencing. In some cases,modulators can be used to inhibit the capture or pre-amplification of apredominant population of nucleic acids, enabling enrichment of thetarget of interest. In some cases, a modulator may be used forsequencing purposes. For example, a modulator can comprise two regionsof specificity—one side of the modulator can recognize a specificconserved region within a targeted genome and the other side of themodulator can be designed to link to a particular element (e.g., animmobilized primer present in the sequencing platform). In some cases,as a result of the modulator interacting simultaneously with both themolecule of interest and the platform, a single nucleic acid moleculecan be isolated and independently analyzed from the pool of nucleicacids.

Platforms

The assays, reactions, and techniques described herein can be performedon any suitable platform, including but not limited to tubes, capillarytubes, droplets, microfluidic devices (e.g., SlipChip devices), wells,well plates, microplates, microfluidic wells, microfluidic droplets,emulsions, solid supports (e.g., beads or microarrays), microchips, orgels (e.g., 2D gels, 3D gels) and reactions inside gels including“polonies” as in polony PCR on surfaces and in gels.

Platforms can comprise fluid handling mechanisms enabling loading,unloading, mixing, and other handling of sample volumes, reagentvolumes, and other fluids. For example, a microfluidic device can beused comprising channels for loading fluids into wells or droplets, formixing contents of wells or droplets, or for off-loading of contents ofwells or droplets.

Some platforms are useful for conducting assays in a digital orquasi-digital format, as described herein. For example, wells, wellplates, microwells, microfluidic droplets, emulsions, beads, andmicroarrays can provide a useful platform for conducting a digital orquasi-digital assay. In such an assay, the compartments can compriseindividual wells, droplets, beads, or microarray spots.

Platforms can be compatible with one or more readout or detectionmechanisms. For example, a platform can be transparent or translucent inpart or in total, allowing fluorescent measurement, detection ofprecipitate or gas bubble, or other visual observation. A platform cancomprise visual detectors, such as CCDs, CMOS sensors, cameras, photondetectors, and other sensors. In another example, a platform cancomprise electrical sensors, such as electrodes positioned withinmicrowells. Platforms can be compatible with off-loading of samples foranalysis. For example, a platform can permit unloading of droplets orcontents of wells for mass spectrometry, sequencing, or electrophoresis.

Applications

An assay can be conducted in less than or equal to about 600 minutes,540 minutes, 480 minutes, 420 minutes, 360 minutes, 300 minutes, 240minutes, 180 minutes, 120 minutes, 110 minutes, 100 minutes, 90 minutes,80 minutes, 70 minutes, 60 minutes, 50 minutes, 40 minutes, 30 minutes,20 minutes, 15 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6minutes, 5 minutes, 4 minutes, 3 minutes, 2 minutes, or 1 minute. Anassay can have an accuracy of at least about 50%, 60%, 70%, 80%, 90%,95%, 96%, 97%, 98%, 99%, 99.9%, or 99.99%. The rates of false positivescan be below 10%, below 1%, below 0.1%, below 0.01%, below 0.001%, orbelow 0.0001%. The rates of false negatives can be below 10%, below 1%,below 0.1%, below 0.01%, below 0.001%, or below 0.0001%.

Assays can be used for single-nucleotide polymorphism (SNP) detection ordiscovery. DNA sequence variations can occur when a single nucleotide ina genome or other shared sequence differs between members of abiological species, or between paired chromosomes in a human. When aspecific restriction enzyme pattern or genetic fingerprint has beenestablished (e.g., as described herein), any change to it (e.g., newnegative reactions) can indicate a modification in the sequence of theproduced amplicons, from a SNP to a chromosome level change.

Assays can be used for detecting copy number variations (CNVs). CNVs area form of structural variation, alterations of the DNA of a genome thatchanges the number of copies of one or more sections of the DNA. CNVscan correspond to relatively large regions of the genome that have beendeleted or duplicated on certain chromosomes. Like other types ofgenetic variation, some CNVs have been associated with susceptibility orresistance to disease. Gene copy number can be elevated in cancer cells.The methodology described herein also allows identifying genetic changesat chromosome level.

An assay can be used for quantitative detection of nucleic acids, suchas Hepatitis C RNA. For example, a method can be used comprising thesteps of taking a sample from the patient, accessing RNA in the sampleor extracting RNA from the sample, using at least one RT-LAMP primer setas set out in Table 10 to reverse transcribe and amplify the RNA in aqualitative and/or in a quantitative format, and testing foramplification to confirm presence of nucleic acids including but notlimited to Hepatitis C RNA.

Assays can be used for genotyping, i.e. determining differences in thegenetic make-up (genotype) of an organism or group of organisms byexamining the DNA or RNA sequence and comparing it to a referencesequence. This can be used to define biological populations by use ofmolecular tools. For example, Example 1 shows three differentrestriction enzymes (BsrBI, BstNI and NheI) used to classify differenthepatitis C virus (HCV) samples into the genotype level, from genotype 1to genotype 4. Subtyping of HCV can also be achieved using thismethodology. HCV subtype 1a and 1b are reported to have differentresponse to therapy (see, e.g., “A M Pellicelli, M Romano, TStroffolini, E Mazzoni, F Mecenate, R Monarca, A Picardi, M EBonaventura, C Mastropietro, P Vignally, A Andreoli, M Marignani, CD'Ambrosio, L Miglioresi, L Nosotti, O Mitidieri, U V Gentilucci, CPuoti, G Barbaro, A Barlattani, C Furlan, G Barbarini, BMCGastroenterol. 2012 Nov. 16; 12:162”), and for the CLEO Group, HCVGenotype 1a shows a better virological response to antiviral therapythan HCV Genotype 1b. As a result, differentiating Genotype 1a fromGenotype 1b can be clinically important. Using the same priming regiondescribed in Example 1, subtyping can be achieved with restrictionenzyme BcoDI, as shown in FIG. 5A. Other restriction enzyme candidatesare available for subtyping to target other regions of the HCV genome,such as NS5b or CORE. For example, Hpy99I, BstNI and BssSI, amongothers, are good candidates for 1a/1b subtyping in the HCV CORE regionas shown in FIG. 5B.

Assays can be used for detecting epigenetic marks or modifications(e.g., methylation, glycosylation, hydroxymethylation): Epigeneticmodifications can comprise functionally relevant modifications to thegenome that do not involve a change in the nucleotide sequence.Methylation of DNA is a common epigenetic signaling tool and is animportant component in numerous cellular processes (e.g., embryonicdevelopment, genomic imprinting, X-chromosome inactivation). Errors inmethylation are linked to a variety of devastating consequences,including several human diseases. Furthermore, adenine or cytosinemethylation is part of the restriction modification system of manybacteria, in which specific DNA sequences are methylated periodically.Foreign DNAs, which are not methylated in this manner, that areintroduced into the cell are degraded by sequence-specific restrictionenzymes and cleaved (while bacterial genomic DNA is not recognized bythese restriction enzymes). The methylation of native DNA can act as asort of primitive immune system, allowing the bacteria to protectthemselves from infection by bacteriophage. As an example of thisapplication, when restriction enzyme recognition sites are methylated,DNA cleavage can be blocked, depending on the restriction enzyme; themethodologies presented herein can detect and identify such methylation.In another example, some restriction enzymes depend on methylation andhydroxymethylation for cleavage to occur (e.g., EpiMark®);methylation-dependent restriction enzyme activity (both positive andnegative) can be used to map epigenetic modifications and study DNAmethylations. Epigenetic analysis can be accomplished using themethodologies described herein.

Assays can be used for identification of mutations, such as drugresistance mutations (DRM). Drug resistance can be achieved by multiplemechanisms, including horizontal acquisition of resistance genes(carried by plasmids or transposons), by recombination of foreign DNAinto the chromosome, or by mutations in different chromosomal loci. Themethodologies described herein can be used for the identification of acharacteristic restriction enzyme pattern or fingerprint, or theactivity of specific restriction enzymes, associated with mutations thatconfer drug resistance. For example, an assay can be used for diagnosisof Methicillin-resistant Staphylococcus aureus (MRSA): MRSA is apathogen responsible for a wide spectrum of healthcare-associated andcommunity-acquired infections. Infections with MRSA strains that areresistant to different types of antibiotics are a serious therapeuticproblem, because only a limited spectrum of antibiotics can be used, andtreatment can require prolonged hospitalization and result in economiclosses. In order to limit the overspread of pathogens, the developmentof diagnostic tools enabling rapid identification of carriers andinfected patients, also enabling livestock and food supply screening andtesting, may be accomplished using the methodologies described herein.

Assays can be used to screen for transgene integration. A transgenicorganism has in its cells a foreign gene that has been inserted bylaboratory techniques or inherited from a transgenic parent organism.Transgenic organisms can be produced by introducing cloned genes,composed of DNA from microbes, animals, or plants, into plant and animalcells. Transgenic technology affords methods that allow the transfer ofgenes between different species. Identification of a geneticallymodified organism (e.g., food or laboratory animals) may be accomplishedusing the methodologies described herein.

Assays can be used for detection of restriction enzyme activity,identifying new restriction enzymes, or evaluating restriction enzymeactivity. As explained in “Julie K. A. Kasarjian, Yoshiaki Kodama,Masatake Iida, Katsura Matsuda, and Junichi Ryu, Four new type Irestriction enzymes identified in Escherichia coli clinical isolates,Nucleic Acids Res. 2005; 33(13): e114,” the recognition sequences fortype II enzymes are relatively easy to identify using crude extracts todigest fixed DNA sequences to produce distinct DNA bands; sequences canthen be predicted using a computer program, such as REBpredictor (NewEngland BioLabs). However, no simple method has been identified forfinding type I recognition sequences, in part because the enzymesproduce DNA fragments with random sequences (TA Bickle and DH Kruger,Biology of DNA Restriction, Microbiol. Rev. 1993; 57:434-450).Identification of new restriction enzymes or analysis of restrictionenzyme target sequences can be accomplished using the methodologiesdescribed herein. For example, amplification reactions can be conductedon different template nucleic acid sequences in the presence of arestriction enzyme modulator, and the effect (e.g., reduced efficiencyor rate) of the modulator can be observed and correlated to particularsequences.

Assays can be used to subtype or characterize strains of viruses. Forexample, there are three types of influenza viruses: A, B and C. Humaninfluenza A and B viruses cause seasonal epidemics. Influenza A virusesare hosted by numerous avian and mammalian (humans, pigs, horses, dogs,marine mammals and others) species, with a viral genome consisting ofeight RNA segments that are frequently exchanged between differentviruses via a process known as genetic reassortment. Influenza type Aviruses are categorized into subtypes based on the type of two proteinson the surface of the viral envelope, H (hemagglutinin, a protein thatcauses red blood cells to agglutinate) and N (neuraminidase, an enzymethat cleaves the glycosidic bonds of the monosaccharide, neuraminicacid). Different influenza viruses encode for different hemagglutininand neuraminidase proteins. For example, the H5N1 virus designates aninfluenza A subtype that has a type 5 hemagglutinin (H) protein and atype 1 neuraminidase (N) protein. Influenza A subtypes found in humansinclude H1N1, H2N2, H3N2, H5N1, H7N7, H1N2, H9N2, H7N2, H7N3, H10N7 andH7N9. The methodologies described herein can be used for rapid andaccurate identification and screening of targets (e.g., influenzavirus). An assay can be conducted in less than or equal to about 600minutes, 540 minutes, 480 minutes, 420 minutes, 360 minutes, 300minutes, 240 minutes, 180 minutes, 120 minutes, 110 minutes, 100minutes, 90 minutes, 80 minutes, 70 minutes, 60 minutes, 50 minutes, 40minutes, 30 minutes, 20 minutes, 15 minutes, 10 minutes, 9 minutes, 8minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, 3 minutes, 2minutes, or 1 minute. An assay can have an accuracy of at least about50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 99.99%. Therates of false positives can be below 10%, below 1%, below 0.1%, below0.01%, below 0.001%, or below 0.0001%. The rates of false negatives canbe below 10%, below 1%, below 0.1%, below 0.01%, below 0.001%, or below0.0001%. Methodologies can have applications in pandemic influenza riskmanagement. The methodologies described herein can also be used todetect the emergence of new virus strains, such as new strains ofinfluenza. Current systems for typing and subtyping influenza virusesinclude virus replication in egg or cell culture followed by eitherimmunofluorescence assays with strain-specific monoclonal antibodies orhemagglutination inhibition assays using a panel of reference antisera,which can be tedious and requires several days or even weeks (see M. L.Landry, Diagnostic tests for influenza infection, Curr Opin Pediatr,2011, 23: 91-97). Assays described herein can be used for routinepoint-of-care tests, including subtyping capability useful forsurveillance of diseases.

Assays can comprise amplification of the haemagglutinin (HA) and/orneuraminidase (NA) genes for subtyping, which genes comprise highlyvariable genomic regions that hinder the standardization of molecularmethods. In some cases, HA and NA genes of influenza can be targetedwhile circumventing the need for repeated re-design of primers andprobes. Influenza viruses can be identified detected and monitored byusing the methodologies described herein by targeting sequencessurrounding SNPs that are located in the matrix (M) gene segment, ahighly conserved gene in the influenza genome. The M gene has enoughgenetic diversity for influenza subtyping purposes and sufficientgenetic stability to for detection and typing. To reduce the number ofsequences being targeted in this approach, one can, for example,establish phylogenetic groups based on the M segment that correlate witha group of subtypes, reducing the number of variables to target andpotentially simplifying the analysis of HA and NA segments in theplatform. Sequences for the M gene segment of influenza A and B can becompiled using the Influenza Virus Resource database at the NationalCenter for Biotechnology, the Influenza Research Database, and TheInfluenza Sequence Database at Los Alamos National Laboratory. Ifneeded, sequences for HA and NA gene segments for influenza A can, forexample, be also compiled from the same source. This approach can beused to find genetic markers that are unique to a particular subtype orgroup of subtypes of influenza based on host species. These databasescan in some examples be separated by subtype and host. Phylogeneticreconstruction can be conducted according to the followingbioinformatics pipeline. (i) Alignment: In the alignment step ofphylogenetic reconstruction, the homology of the whole sequences can berefined to identify homologous sites by, for example, placing gaps atsites where insertions or deletions have occurred since the last commonancestor. To perform this step the Prank algorithm as implemented inSATé II (Simultaneous Alignment and Tree Estimation) can be used (see K.Liu, T. J. Warnow, M. T. Holder, S. M. Nelesen, J. Yu, A. P. Stamatakisand C. R. Linder, SATe-II: very fast and accurate simultaneousestimation of multiple sequence alignments and phylogenetic trees, SystBiol, 2012, 61: 90-106). The resulting alignment can, in some cases, bemanually curated to eliminate regions that could have been misaligned(due to, e.g., high variability). (ii) Model selection: Somephylogenetic methods (e.g., maximum likelihood and Bayesian analysis)may benefit from specification of an evolutionary model. In some casesthe model of evolution can be selected using the Akaike informationcriterion and/or Bayesian cross-validation using, for example,jModelTest and PhyloBayes, respectively (see D. Posada, jModelTest:phylogenetic model averaging, Mol Biol Evol, 2008, 25: 1253-1256; and N.Lartillot, T. Lepage and S. Blanquart, PhyloBayes 3: A Bayesian softwarepackage for phylogenetic reconstruction and molecular dating,Bioinformatics, 2009, 25, 2286: 2288). (iii) Phylogeny Reconstruction:In some cases phylogenetic reconstruction can be performed under maximumlikelihood and Bayesian frameworks. Maximum likelihood can be carriedout using RAxML and reliability of nodes can be evaluated usingbootstrapping (see A. Stamatakis, RAxML version 8: a tool forphylogenetic analysis and post-analysis of large phylogenies,Bioinformatics, 2014, doi: 10.1093/bioinformatics/btu033). In someexamples Bayesian analysis can be performed using PhyloBayes. Potentialsources of systematic error can be evaluated using Bayesian posteriorpredictive analysis as implemented in PhyloBayes in order to assess thereliability of the resulting topology, in some examples (See N.Lartillot, T. Lepage and S. Blanquart, PhyloBayes 3: A Bayesian softwarepackage for phylogenetic reconstruction and molecular dating,Bioinformatics, 2009, 25, 2286: 2288). (iv) Genetic marker prediction:Single nucleotide polymorphism detection can involve looking acrossmultiple sequence alignments and identifying base discrepancies. Thehigher the sequence coverage and quality score at a given site, the moreconfident the SNP prediction. In some cases, existing tools (e.g., Phrapor PineSAP) can be used to make confident identifications when visualconfirmation is not an option (See M. Machado, W. C. Magalhaes, A. Sene,B. Araujo, A. C. Faria-Campos, S. J. Chanock, L. Scott, G. Oliveira, E.Tarazona-Santos and M. R. Rodrigues, Phred-Phrap package to analysestools: a pipeline to facilitate population genetics re-sequencingstudies, Investig Genet, 2011, 2, 3 and J. L. Wegrzyn, J. M. Lee, J.Liechty, and D. B. Neale, PineSAP-sequence alignment and identificationpipeline, Bioinformatics, 2009, 25, 2609-2610). Strategies for ensuringlow rates of false positives in subtyping can also be used in someexamples; a test or assay can report not only the subtype but alsoprovide some information on, for example, the confidence of the subtypedesignation. These approaches can be used to create tests with low ratesof false positives, which would be advantageous when millions of peopleare screened. The rates of false positives can be below 10%, below 1%,below 0.1%, below 0.01%, below 0.001%, or below 0.0001%.

While a number of details are provided herein for relating to analysisof influenza, analysis of other viruses (including detection, typing,subtyping, SNP detection, and other analysis) can be performedanalogously. Analysis of Hepatitis viruses, including HCV, HBV, HAV,HIV, HPV, and other viruses of relevance to human health, agriculture,agricultural biotechnology, and other practical applications, can beperformed. Analysis and detection of viral, archaeal, bacterial, fungal,mammalian, human, and other nucleic acids can be performed. Analysis anddetection includes comparative analysis and detection, where a targetnucleic acid is compared with another nucleic acid.

The methodologies described herein can be used to detect otheractivities in conjunction with detection and or amplification such asreactions that make or break chemical bonds, reactions that lead toformation of complexes between molecules, or reactions that lead toformation of complexed between molecules and objects such as beads andsurfaces. The methodologies can be used to detect activation ofdetection or amplification. For example, a protease can be used todegrade at least one peptide bond in a complex between a target nucleicacid and a molecule containing such a peptide bond (e.g., proteins,peptides, and their derivatives). This degradation can causedissociation of the complex between the target nucleic acid and themolecule containing such a peptide bond, enhancing the amplification ordetection of the target nucleic acid. Similarly, a glycosidase can beused to degrade a glycosidic bond, leading to the release of smallsugars. If the release of the small sugar or the degradation of theglycosidic bond leads to the formation or degradation of some complexbetween molecules, it can change the rate of an amplification reactionor allow or prevent an amplification reaction. Glycoside hydrolase canalso be used as synthetic catalysts to form glycosidic bonds througheither reverse hydrolysis. Glycosyltransferases, on the other hand, canestablish natural glycosidic linkages, including the biosynthesis ofdisaccharides, oligosaccharides and polysaccharides.Glycosyltransferases can catalyse the transfer of monosaccharidemoieties from activated nucleotide sugar (also known as the “glycosyldonor”) to a glycosyl acceptor molecule, such as an alcohol. The resultof glycosyl transfer can be a carbohydrate, glycoside, oligosaccharide,or a polysaccharide. Similarly, kinase enzymes can be used to transferphosphate groups from high-energy donor molecules, such as ATP tospecific substrates, a process referred to as phosphorylation, whilephosphorylases can be used to conduct phosphorolysis, the breaking of abond using an inorganic phosphate group. Aptamers can be used to bind tospecific proteins or nucleic acid targets.

Assays can be used to identify drug resistance mutations (DRMs). Drugresistance can be achieved by multiple mechanisms, including but notlimited to horizontal acquisition of resistance genes (carried byplasmids or transposons), by recombination of foreign DNA into thechromosome, or by mutations in different chromosomal loci. Theidentification of a characteristic restriction enzyme pattern or theactivity of specific restriction enzymes associated with mutations thatconfer drug resistance can, in some cases, be accomplished using themethodologies described herein. Drug resistance can be determined usingthe methodologies described herein in subjects including but not limitedto viruses, bacteria, fungi, plants, prokaryotes, and eukaryotes. Thesemutations can also be determined in, e.g., cancer cells and cell-freeDNA. For example, this can be applied to identify drug resistancemutations in HCV (see, e.g., “Clinically Relevant HCV Drug ResistanceMutations Figures and Tables, from HCV Phenotype Working Group, HCV DrugDevelopment Adivosry Group, Ann Forum Collab HIV Res. Volume 14 (2):2012; 1-10” or “Forum for Collaborative HIV Research, University ofCalifornia Berkeley School of Public Health”), HIV (see, e.g., “VictoriaA. Johnson, MD, Vincent Calvez, MD, PhD, Huldrych F. Günthard, MD, RogerParedes, MD, PhD, Deenan Pillay, MD, PhD, Robert W. Shafer, MD,Annemarie M. Wensing, MD, PhD, and Douglas D. Richman, MD, Update of theDrug Resistance Mutations in HIV-1: March 2013, Topics in AntiviralMedicine, 2013; 21:6-14”), and influenza A virus (see, e.g., “GoranOrozovic, Kanita Orozovic, Johan Lennerstrand, Bjorn Olsen, Detection ofResistance Mutations to Antivirals Oseltamivir and Zanamivir in AvianInfluenza A Viruses Isolated from Wild Birds. PLoS ONE 6(1): e16028.doi:10.1371/journal.pone.0016028”).

Assays can be used for genetic testing, including fetal genetic testing.For example, assays can be used for non-invasive pre-natal Trisomy 21(Down syndrome) diagnostics. Assays can be used with a screening testwhich indicates the likelihood of trisomy. Assays can be used with or asa screening test for a subsequent diagnostic test which is a moreaccurate test provided only to people with a high score in the screeningtest. A screening test can comprise an ultrasound test. A screening testcan comprise a maternal serum screening blood test measuring the levelof human chorionic gonadotropin (β-hCG), pregnancy associated plasmaprotein-A (PAPP-A), alpha fetoprotein (AFP), or other proteinbiomarkers. A screening test can provide a probability instead of afinite answer. If the screening test gives a high score, an invasivediagnostic test, such as chorionic villus sampling (CVS) oramniocentesis, can be used. Cell-free fetal DNA (cff DNA) or RNA (cffRNA) exist in maternal plasma that can be isolated and subjected tomolecular analysis (see, e.g., “Y M Dennis Lo, Noemi Corbetta, Paul FChamberlain, Vik Rai, Ian L Sargent, Christopher W G Redman, James SWainscoat, Presence of fetal DNA in maternal plasma and serum, Lancet1997, 350, 485-487”). The cff DNA and cff RNA can be used in assays fornon-invasive biomarker discovery and detection. For cff DNA, abiological and therefore technical constraint is that it only takes up3-6% of the total amount of cell-free DNA. The proportion increases at alater stage of gestation, but is still a minor fraction of the totalamount of cell-free DNA in plasma. Assays can directly targetfetal-specific DNA or RNA. The placenta is an organ that can representgenetic information from the fetus. Placental-specific RNA, whenexpressed and released in a tissue-specific manner, qualifies as afetal-specific RNA because it exists only in pregnant individuals anddoes not exist before or after pregnancy. Assays can comprise detectionof trisomy 21 using placental specific RNA by direct dosage-relateddifference in the expression of chromosome 21 encoded genes (see, e.g.,“Chi-Ming Li, Meirong Guol, Martha Salas, Nicole Schupf, WayneSilverman, Warren B Zigman, Sameera Husain, Dorothy Warburton,Harshwardhan Thaker, and Benjamin Tycko, “Cell type-specificover-expression of chromosome 21 genes in fibroblasts and fetal heartswith trisomy 21” BMC Medical Genetics 2006, 7: 24″). Assays can comprisedetection of trisomy 21 using placental specific RNA by relative RNAallelic ratio assessment using SNP analysis (see, e.g., “Y M Dennis Lo.,Nancy B Y Tsui, Rossa W K Chiu, Tze K Lau, Tse N Leung, Macy M S Heung,Egeliki Gerovassili, Yongjie Jin, Kypros H Nicolaides, Charles R Cantor,and Chunming Ding, Plasma placental RNA allelic ratio permitsnoninvasive prenatal chromosomal aneuploidy detection, Nat. Med. 2007,13, 218”). Relative RNA allelic ratio assessment using SNP analysis canquantify the relative abundance of each allele in expressed placentalspecific RNA when there is a heterozygous loci on chromosome 21 genes,with the assumption that the ratio of the two alleles for motherscarrying a trisomy 21 baby should be 2:1, and for a normal baby itshould be 1:1. Since only a relative ratio is required, the number ofwells or other partitions can be small if digital PCR is used in such anassay.

Described herein is an exemplary a rapid assay not requiring CVS oramniocentesis that can be used as a screening test or a diagnostic testwith high sensitivity and specificity based on, in one example, RNA SNPquantification on chromosome 21. In some cases, this platform can havethe capacity for collecting sample and purifying RNA out of the plasmasample, multiplexed SNP ratio quantification, and a relatively simplereadout module, including but not limited to one that is cell-phoneenabled. The results can be interpretable by, for example, the user orthe physician, and in some cases can be offered together withconsultation service at the clinic, to help parents make decisions andprepare. Assay coverage can be at least about 50%, 60%, 70%, 80%, 90%,95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, or 100%. An assay can be used incombination with another screening test and can decrease the number offalse-positives in the screening test. An assay can provide access tosuch tests to people who do not currently have access. The developmentof such a platform can fill the gaps between the large demand fortrisomy 21 detection and limited access to diagnostics. In one exampleof this platform, a sample (such as, for example, human blood) can becollected and loaded onto the integrated device. In some cases, thesample can flow to merge with different reagents to complete the RNAextraction step driven by, for example, pressure. In some cases, the RNAcan then be mixed with isothermal amplification reagents containing, forexample, different inhibitors specific to different alleles. In somecases, after rapid sequence specific amplification, the digital countsfor different reactions can be recorded (such as, for example, by a cellphone, which can have a built-in analysis application). In some cases,the assay can comprise a SNP assay for multiple loci, increasing thepopulation coverage of the entire assay. In some cases, proper controland potentially other trisomy detection assays can be included as well.In some cases, for heterozygous loci, the ratio between the two allelesshould be 1:1 for euploidy, while that for aneuploidy should be about2:1. In some cases, for homozygous loci, only one allele will bedetected. FIG. 16 shows a schematic of an exemplary prenatal diagnostictest. In FIG. 16A, results are shown for a sample, heterozygous at locusB, negative (upper) and positive (lower) for trisomy. Both show asimilar number of positive signals for the ‘B’ SNP assay, and the samplepositive for trisomy shows more positive signals for the ‘b’ SNP assay.In FIG. 16B, results are shown for a sample, homozygous at locus A,negative (upper) and positive (lower) for trisomy. Both show no positivesignals for the ‘a’ SNP assay, and the sample positive for trisomy showsmore positive signals for the ‘A’ SNP assay. Genetic testing (prenatalor postnatal) can be used to screen for other aneuploidy conditionsincluding but not limited to Edwards syndrome (Trisomy 18) and Patausyndrome (Trisomy 13). Genetic testing can be used to screen for othergenetic conditions including but not limited to phenylketonuria andcongenital hypothyroidism. Genetic testing can also be used to study orpredict drug metabolism (e.g., SNPs and other mutations in the liverP450 cytochrome system of enzymes including CYP2C9, CYP2C19, CYP3A4, andCYP1A2).

Assays can be used for epigenetic testing for diseases and otherconditions, including but not limited to Angelman syndrome, Prader-Willisyndrome, Beckwith-Wiedemann syndrome, aberrant DNA methylationassociated with cancer (hypermethylation, e.g. at CpG islands in thepromoter region or hypomethylation, e.g. global hypomethylation),epigenetic changes (e.g., CpG island methylation) associated withreduced expression of DNA repair genes (e.g., BRCA1, WRN, FANCF, RAD51C,MGMT, MLH1, MSH2, ERCC1, Xpf, NEIL1, FANCB, MSH4, ATM), and varianthistones.

Nucleic acid amplification based on universal set of primers targetingcommon sequences among bacteria or among fungi can be used, for example,to evaluate microbial colonization. Common sequences can include 16Sribosomal RNA or 23S ribosomal RNA in bacteria and 18S ribosomal RNA or28S ribosomal rRNA genes in fungi. Addition of sequence-specificmodulators into these universal PCR systems can be used for bacterial orfungal typing (ribotyping). Ribotyping mediated by modulators can beused, for example, for environmental testing (water, soil, waste, fueland air) with bacteria including but not limited to Escherichia coli,Bacillus subtilis, Clostridum perfringens, Clostridium difficile,Enterobacter aerogenes, Enterococcus faecalis, Legionella pneumophila,Legionella bozemanii, Listeria monocytogenes, Pseudomonas aeruginosa,Salmonella typhimurium, Staphylococcus aureus, and others. Assays can beused for detection of multidrug-resistant organisms (such asStaphylococcus aureus, Klebsiella pneumoniae, Acinetobacter spp.,Enterococcus spp. and Enterobacter spp). Assays can be used fordetection or identification of sulfate reducing organisms or otherorganisms which can lead to pipeline corrosion. A sample can be takenfrom a pipeline, an gut of an organism, or another source.

Assays can be used to identify or characterize mobile genetic elements(e.g., transposons and bacteriophages) or foreign genes inserted bylaboratory techniques (e.g., genes inserted into genetically modifiedorganisms). For example, when an amplification reaction targeting asequence surrounding an inserted gene, the reaction can be inhibited orpromoted in the presence of a modulator that interacts with the foreigngene. If the foreign gene is not present, the modulator does notsignificantly act and the amplification reaction can proceed withoutsubstantial change to the rate or efficiency of amplification.Approaches described herein can be used for agricultural biotechnology,to detect genes transfected into plants, animals and microorganisms. Inanother example, virulence factors of pathogenic bacteria encoded bypathogenicity islands (PAI) can be assessed. PAI carry genes encodingone or more virulent factors, including but not limited to, adhesins,toxins, invasins, protein secretion systems, iron uptake systems, andothers. PAI comprise genomic regions that are present on the genomes ofpathogenic strains but absent or only rarely present in thosenon-pathogenic variants of the same related species. An amplificationreaction can be triggered, for example, by the presence a specific PAI.For example, an amplification reaction can be blocked by a modulator,and in the presence of a specific sequence contained in the PAI themodulator can be removed and the amplification reaction can beinitialized. The presence of transferred genes (or transferredgeneomictic islands) can also be used in combination with a modulator,for example with pathogenic bacteria such as Escherichia spp., Shigellaspp., Yersinia spp., Vibrio spp., Clostridium spp., Haemophilus spp.,Helicobacter spp., Neisseria spp., Pseudomonas spp., Mycobacterium spp.and others.

Assays can be used identification of single point mutations, for examplefor viral genotyping. Genotyped viruses can include but are not limitedto hepatitis C virus, hepatitis B virus, human immunodeficiency virus,human cytomegalovirus, norovirus and enterovirus. Assays can be used forviral typing and subtyping. Typed or subtyped viruses can include butare not limited to human papilloma virus, avian influenza virus, humaninfluenza virus, swine influenza virus, herpes simplex virus, foot andmouth disease virus, dengue virus and rotavirus. Assays can be used forbacterial typing. Typed bacteria can include but are not limited toFrancisella spp., Escherichia spp., Salmonella spp., Mycobacterium spp.,Bacillus spp., Staphylococcus spp., Streptococcus spp., Acinetobacterspp., Helicobacter spp., Bordetella spp., Bordetella spp. and Vibriospp. Assays can be used to assess for the presence or absence of drugresistance mutations, in subjects including but not limited to humanimmunodeficiency virus, hepatitis C virus, and cancer drug resistance.

Control Systems

The present disclosure provides computer control systems that can beemployed to conduct, regulate, analyze, communicate results from, orotherwise control assays and systems provided herein. FIG. 6 shows acomputer system 601 that is programmed or otherwise configured toregulate or analyze assays. The computer system 601 can regulate, forexample, fluid handling for conducting an assay, data collection ofreal-time reaction rates or end-point reaction outcomes, analysis ofdata, and transmission or display of data or results.

The computer system 601 includes a central processing unit (CPU, also“processor” and “computer processor” herein) 605, which can be a singlecore or multi core processor, or a plurality of processors for parallelprocessing. The computer system 601 also includes memory or memorylocation 610 (e.g., random-access memory, read-only memory, flashmemory), electronic storage unit 615 (e.g., hard disk), communicationinterface 620 (e.g., network adapter) for communicating with one or moreother systems, and peripheral devices 625, such as cache, other memory,data storage and/or electronic display adapters. The memory 610, storageunit 615, interface 620 and peripheral devices 625 are in communicationwith the CPU 605 through a communication bus (solid lines), such as amotherboard. The storage unit 615 can be a data storage unit (or datarepository) for storing data.

The CPU 605 can execute a sequence of machine-readable instructions,which can be embodied in a program or software. The instructions may bestored in a memory location, such as the memory 610. Examples ofoperations performed by the CPU 605 can include fetch, decode, execute,and writeback.

The storage unit 615 can store files, such as drivers, libraries andsaved programs. The storage unit 615 can store programs generated byusers and recorded sessions, as well as output(s) associated with theprograms. The storage unit 615 can store user data, e.g., userpreferences and user programs. The computer system 601 in some cases caninclude one or more additional data storage units that are external tothe computer system 601, such as located on a remote server that is incommunication with the computer system 601 through an intranet or theInternet.

The computer system 601 can be in communication with an assay system630, including various elements of the assay system. Such elements caninclude sensors, fluid handling mechanisms (e.g., motors, valves,pumps), and actuators.

Methods as described herein can be implemented by way of machine (e.g.,computer processor) executable code stored on an electronic storagelocation of the computer system 601, such as, for example, on the memory610 or electronic storage unit 615. The machine executable or machinereadable code can be provided in the form of software. During use, thecode can be executed by the processor 605. In some cases, the code canbe retrieved from the storage unit 615 and stored on the memory 610 forready access by the processor 605. In some situations, the electronicstorage unit 615 can be precluded, and machine-executable instructionsare stored on memory 610.

The code can be pre-compiled and configured for use with a machine havea processer adapted to execute the code, or can be compiled duringruntime. The code can be supplied in a programming language that can beselected to enable the code to execute in a pre-compiled or as-compiledfashion.

Aspects of the systems and methods provided herein, such as the computersystem 601, can be embodied in programming Various aspects of thetechnology may be thought of as “products” or “articles of manufacture”typically in the form of machine (or processor) executable code and/orassociated data that is carried on or embodied in a type of machinereadable medium. Machine-executable code can be stored on an electronicstorage unit, such memory (e.g., read-only memory, random-access memory,flash memory) or a hard disk. “Storage” type media can include any orall of the tangible memory of the computers, processors or the like, orassociated modules thereof, such as various semiconductor memories, tapedrives, disk drives and the like, which may provide non-transitorystorage at any time for the software programming. All or portions of thesoftware may at times be communicated through the Internet or variousother telecommunication networks. Such communications, for example, mayenable loading of the software from one computer or processor intoanother, for example, from a management server or host computer into thecomputer platform of an application server. Thus, another type of mediathat may bear the software elements includes optical, electrical andelectromagnetic waves, such as used across physical interfaces betweenlocal devices, through wired and optical landline networks and overvarious air-links. The physical elements that carry such waves, such aswired or wireless links, optical links or the like, also may beconsidered as media bearing the software. As used herein, unlessrestricted to non-transitory, tangible “storage” media, terms such ascomputer or machine “readable medium” refer to any medium thatparticipates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, a tangible storagemedium, a carrier wave medium or physical transmission medium.Non-volatile storage media include, for example, optical or magneticdisks, such as any of the storage devices in any computer(s) or thelike, such as may be used to implement the databases, etc. shown in thedrawings. Volatile storage media include dynamic memory, such as mainmemory of such a computer platform. Tangible transmission media includecoaxial cables; copper wire and fiber optics, including the wires thatcomprise a bus within a computer system. Carrier-wave transmission mediamay take the form of electric or electromagnetic signals, or acoustic orlight waves such as those generated during radio frequency (RF) andinfrared (IR) data communications. Common forms of computer-readablemedia therefore include for example: a floppy disk, a flexible disk,hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD orDVD-ROM, any other optical medium, punch cards paper tape, any otherphysical storage medium with patterns of holes, a RAM, a ROM, a PROM andEPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wavetransporting data or instructions, cables or links transporting such acarrier wave, or any other medium from which a computer may readprogramming code and/or data. Many of these forms of computer readablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processor for execution.

EXAMPLES Example 1—Real-Time Bulk HCV Genotyping Results Using RT-LAMPand Restriction Enzymes

Three restriction enzymes (BsrBI, NehI, and BstNI) were selected basedon hepatitis C virus (HCV) sequence and its variation in differentgenotypes. A set of customized LAMP primers targeting 5′UTR weredesigned. This set of primers was optimized to show high amplificationefficiency for genotype 1, 2, 3 and 4. The cutting site of therestriction enzyme is inside the priming region (between B3 and F3; seeTsugunori Notomi, Hiroto Okayama, Harumi Masubuchi, Toshihiro Yonekawa,Keiko Watanabe, Nobuyuki Amino and Tetsu Hase, “Loop-mediated isothermalamplification of DNA”, Nucleic Acids Res. 2000 Jun. 15; 28(12):E63), sothat the enzyme cuts the product during amplification and leads to theinhibition or delay of the reaction. The alignment of RNA sequence,priming region and digestion site for NheI, BstNI, BsrBI, BsrI, andBcoDI is shown in FIG. 5A. The digestion site for the enzymes isspecific to different genotypes so each enzyme specifically cuts certaingenotypes. For example, the sequence which BsrBI cuts is CCGCTC, whichwith these RT-LAMP primers only exists in the amplicon of genotype 1, 3and 4. As a result, the LAMP reaction with BsrBI is expected to bepositive only for genotype 2. Based on the specificity of the enzymes,the predicted amplification pattern of LAMP-RE is shown in FIG. 7. Forexample, the digestion site for Hpy99I (A) only exists in the ampliconof subtype 1a, the digestion site for BstNI (B) only exists in subtype1b, and BssSI (C) only digests the amplicon of subtype 1b; therefore,the combination of these enzymes enables the identification of subtype1a and 1b. The expected pattern of positive and negative reactionresults is shown in FIG. 7; each row stands for one HCV RNA genotype,each column stands for one restriction enzyme, black stands for“positive or not-delayed reaction,” and white stands for “negative ordelayed reaction.” The time required for the LAMP reaction to changefrom negative (below intensity threshold) to positive (above intensitythreshold) is shown in FIG. 8; positive controls are experiments in theabsence of restriction enzyme, shown in solid grey as reference.Different restriction enzymes exhibit different capability fordigestion, which results in different extent of delay. All experimentswere performed in triplicates, with p-value shown above each bar in FIG.8. In the real-time experiment, each cycle was set to be 1 minute andthe fluorescence intensity was measured at the end of each cycle. Due tothe time required for imaging (12 s per cycle), the cycle numbers didnot reflect the absolute reaction time in the unit of minute. Real timeRT-LAMP for HCV genotype 1 showed a significant delay (later time topositive than the positive control, last row) when it was combined withBsrBI, NehI, BstNI. For genotype 2, delayed reaction was observed withNehI. For Genotype 3 reaction with BsrBI was delayed and for genotype 4with BsrBI and NehI.

To amplify HCV viral RNA using an RT-LAMP method on a real-time PCRmachine without restriction enzymes, the RT-LAMP mix contained thefollowing: 20 μL of RM, 2 μL of EM, 1 μL of FD, 4 μL of primer mixture(20 μM BIP/FIP, 10 μM LooP_B/Loop_F, and 2.5 μM B3/F3), various amountsof RNA template solution, and enough nuclease-free water to bring thevolume to 40 μL. The solution was split into 10 μL each and loaded into3 wells on the Eco real-time PCR (Illumina, CA) plate and heated at 63°C. for 50 min.

To amplify HCV viral RNA using RT-LAMP in the presence of restrictionenzymes on a real-time PCR machine, the RT-LAMP mix contained thefollowing: 20 μL of RM, 2 μL of EM, 1 μL of FD, 4 μL of primer mixture(20 μM BIP/FIP, 10 μM LooP_B/Loop_F, and 2.5 μM B3/F3), various amountsof RNA template solution, 4 μL diluted RE (20 fold diluted frompurchased stock solution) and enough nuclease-free water to bring thevolume to 40 μL. The solution was split into 10 μL each and loaded into3 wells on the Eco real-time PCR plate and heated at 63° C. for 50 min.

Example 2—End-Point Digital HCV Genotyping Results Using RT-LAMP andRestriction Enzymes

Digestion was performed during amplification reaction for hepatitis Cvirus (HCV) RNA on a SlipChip platform. Digital RT-LAMP for HCV RNA wasmore thoroughly inhibited at the single RNA level compared to a bulkassay, as shown for example in FIG. 9 and FIG. 10. FIG. 9 shows digitalRT-LAMP results with and without restriction enzymes for HCV genotyping.Positive controls are experiments in the absence of restriction enzyme,shown in solid grey as reference. Different restriction enzymes exhibitdifferent capabilities for digestion, which results in different countsamong genotypes. All experiments were performed in triplicates, with thep value shown above each bar. FIG. 10 shows digital RT-LAMP results(black dots are positive counts) on a SlipChip platform with genotype1-4 HCV RNA and different restriction enzymes—NheI (fourth row), BsrBI(third row), and BstNI (second row)—as well as a positive control (firstrow). Digital RT-LAMP for HCV Genotype 1 RNA was inhibited by BsrBI,NheI, and BstNI at the single RNA level. Digital RT-LAMP for Genotype 2RNA was only inhibited by NheI. Digital RT-LAMP for HCV Genotype 3 wasonly inhibited by BsrBI. Digital RT-LAMP for HCV Genotype 4 RNA wasinhibited by both BsrBI and NheI. These results conform with thepredicted pattern of inhibition based on genotype sequences andrestriction enzyme targeting.

The SlipChip device used was single volume 1280-well device, designedand optimized based on “Bing Sun, Feng Shen, Stephanie E. McCalla, JasonE. Kreutz, Mikhail A. Karymov, and Rustem F. Ismagilov. Mechanisticevaluation of the pros and cons of digital RT-LAMP for HIV-1 viral loadquantification on a microfluidic device and improved efficiency via atwo-step digital protocol. Anal Chem 2013, 85(3): 1540-1546.” Theprocedure of fabricating the SlipChip from soda-lime glass was based onthe procedure described in “Feng Shen, Bing Sun, Jason E. Kreutz, ElenaK. Davydova, Wenbin Du, Poluru L. Reddy, Loren J. Joseph, and Rustem F.Ismagilov, Multiplexed quantification of nucleic acids with largedynamic range using multivolume digital RT-PCR on a rotational SlipChiptested with HIV and hepatitis C viral load. J Am Chem Soc 133(44):17705-17712” and “Wenbin Du, Liang Li, Kevin P. Nichols, and Rustem FIsmagilov, SlipChip, Lab Chip 2009, 9: 2286-2292.” All features wereetched to a depth of 55 um to make the volume of loading well equal to 3nL.

To amplify HCV viral RNA using a RT-LAMP method on a real-time PCRmachine, the RT-LAMP mix contained the following: 20 μL of RM, 2 μL ofEM, 1 μL of FD, 4 μL of primer mixture (20 μM BIP/FIP, 10 μMLooP_B/Loop_F, and 2.5 μM B3/F3), 2 μL of BSA (20 mg/mL), variousamounts of RNA template solution, 4 μL diluted restriction enzyme(except for positive control), and enough nuclease-free water to bringthe volume to 40 μL. The solution was loaded onto a SlipChip and heatedat 63° C. for 50 min on a house-built real-time instrument. Experimentswere performed on a Bio-Rad PTC-200 thermocycler with a custom machinedblock. The block contains a flat 3″×3″ portion onto which the devicesare placed ensuring optimal thermal contact. The excitation light sourceused was a Philips Luxeon S (LXS8-PW30) 1315 lumen LED module with aSemrock filter (FF02-475). Image Acquisition was performed with aVX-29MG camera and a Zeiss Macro Planar T F2-100 mm lens. A Semrockfilter (FF01-540) was used as an emission filter. The exposure time wasset to be 500 ms and gain to be 1.

Example 3—Real-Time Digital HCV Genotyping Results Using RT-LAMP andRestriction Enzymes

Experiments were performed as in the Example 2, except a house-builtimaging instrument was used to monitor the reactions in individual wellsof a SlipChip. Images were acquired every minute with an exposure timeof 500 ms and gain of 1. Both counts and time to positive thresholdchanged with the addition of specific restriction enzymes, as shown inFIG. 11A-11L. FIG. 11 shows real-time digital HCV genotyping (genotype1, 2, 3 and 4) results using RT-LAMP and restriction enzymes. The solidcurve with markers in the first quadrant shows real-time monitoredcounts change over time without restriction enzyme, while the dashedcurve with markers in the first quadrant shows real-time monitoredcounts change over time with restriction enzymes. The solid line withoutmarkers in the second quadrant shows time to positive (min) for bulkexperiments without restriction enzymes, while the dashed line withoutmarkers in the second quadrant is time to positive (min) for bulkexperiments with restriction enzymes. FIG. 11A shows real-time digitaland bulk HCV genotyping results for Genotype 1 with and withoutrestriction enzyme NheI. FIG. 11B shows real-time digital and bulk HCVgenotyping results for Genotype 1 with and without restriction enzymeBsrBI. FIG. 11C shows real-time digital and bulk HCV genotyping resultsfor Genotype 1 with and without restriction enzyme BstNI. FIG. 11D showsreal-time digital and bulk HCV genotyping results for Genotype 2 withand without restriction enzyme NheI. FIG. 11E shows real-time digitaland bulk HCV genotyping results for Genotype 2 with and withoutrestriction enzyme BsrBI. FIG. 11F shows real-time digital and bulk HCVgenotyping results for Genotype 2 with and without restriction enzymeBstNI. FIG. 11G shows real-time digital and bulk HCV genotyping resultsfor Genotype 3 with and without restriction enzyme NheI. FIG. 11H showsreal-time digital and bulk HCV genotyping results for Genotype 3 withand without restriction enzyme BsrBI. FIG. 11I shows real-time digitaland bulk HCV genotyping results for Genotype 3 with and withoutrestriction enzyme BstNI. FIG. 11J shows real-time digital and bulk HCVgenotyping results for Genotype 4 with and without restriction enzymeNheI. FIG. 11K shows real-time digital and bulk HCV genotyping resultsfor Genotype 4 with and without restriction enzyme BsrBI. FIG. 11L showsreal-time digital and bulk HCV genotyping results for Genotype 4 withand without restriction enzyme BstNI. Real time digital traces can beanalyzed in multiple ways in this methodology, including end-pointanalysis, time-course analysis, analysis of the area-under-the-curve,and so forth.

Example 4—Using Oligonucleotide Inhibitors to Selectively Delay a HCVLAMP Amplification Reaction

Two oligonucleotide inhibitors were designed with the same sequenceexcept at four mutation points (underlined). The four mutations wereintroduced in such a way that the melting temperatures (Tm) of the twooligonucleotides (hybridized to DNA) are the same. The sequences of theoligonucleotides are:

Matched inhibitor: (Seq ID No: 6)CGGGGCACTCGCAAGCACCCTATCAGGCAGTACCACAAGGCCTTTCGCGA CCCAACTGATMismatched inhibitor: (Seq ID No: 7)CGGGGCACTCGCAAGCACTCTACCAGACAGTGCCACAAGGCCTTTCGCGA CCCAACTGAT

The results have been summarized in Table 1:

TABLE 1 Time-to-positive results for real-time RT-LAMP with differentoligonucleotide inhibitors for HCV RNA Sample Time to positive/cycle(std. dev.) Positive Control 17.8 (0.23) With matched inhibitor 31.9(0.79) With mismatched inhibitor 23.1 (0.16) (4 mismatches) Neg Ctrl. 54.3 (13.38)

Here time-to-positive is defined as the time required for the LAMPreaction to change from negative (below intensity threshold) to positive(above intensity threshold). In the real-time experiment, each cycle wasset to be 1 minute and the fluorescence intensity was measured at theend of each cycle. Due to the time required for imaging (12 s percycle), the cycle numbers did not reflect the absolute reaction time inthe unit of minute.

Both matched and mismatched inhibitors have delayed the reaction;however the mismatched inhibitors displayed less inhibition effect, asexpected. The matched and mismatched primers were specific (perfectlymatched) to different genotypes, resulting in different inhibitioneffect to the same RNA. This difference leads to a differentiationbetween genotypes. This difference led to the differentiation betweengenotypes. For example, in the reaction where there was oligonucleotideinhibitor specific to Genotype 1 (matched inhibitor in this example),when Genotype 1 HCV RNA was introduced into the reaction a stronginhibition was observed. When the inhibitor is not specific to Genotype1 (such as the mismatched inhibitor in this example) or is specific toother genotypes, when Genotype 1 HCV RNA was introduced, littleinhibition was observed.

To amplify HCV RNA one-step RT-LAMP with oligonucleotide inhibitors, pereach 40 μL the RT-LAMP mix contained the following: 20 μL of RM, 2 μL ofBSA (20 mg/mL), 2 μL of EM, 1 μL of FD, 4 μL of primer mixture (20 μMBIP/FIP, 10 μM LooP_B/Loop_F, and 2.5 μM B3/F3), 2 μL of RNase Inhibitor(20 U/μl), 4 μL of HCV genotype 1 RNA, 1 μL of 80 μM oligonucleotideinhibitor, and enough nuclease-free water to bring the volume to 40 μL.The RNA was extracted from 140 μL of plasma (AcroMetrix® HCV GenotypingPanel) using QIAamp Viral RNA Mini Kit (Qiagen) with an elution volumeof 60 μL. Loopamp® RT-LAMP mix was purchased from SA Scientific. Thesolution was split into 10 μL each and loaded onto Eco real-time PCRmachine and heated at 63° C. for 60 cycles (1 min/cycle).

Example 5—Using Oligonucleotide Inhibitors Together with RT-LAMPReaction for HCV RNA Genotype 1 in Digital SlipChip Device

An experiment was also performed at single molecule level on a SlipChip,as shown in FIG. 12. The reaction mix as detailed in Example 4 was used.The digital experiments showed improved specificity compared to bulkexperiment. The specific oligonucleotide inhibitor completely or nearlycompletely stopped the reaction (very few counts after reaction), whilethe mismatched oligonucleotide inhibitor did not change the count much(similar number of counts to positive control without inhibitors). FIG.12 shows digital RT-LAMP for HCV RNA Genotype 1 results on SlipChip.Black dots represent positive counts. FIG. 12A shows results withmatched inhibitor, FIG. 12B shows results with mismatched inhibitor, andFIG. 12C shows results from a positive control without inhibitors.

To perform HCV RNA one-step RT-LAMP with oligonucleotide inhibitors on aSlipChip, per each 40 μL the RT-LAMP mix contained the following: 20 μLof RM, 2 μL of BSA (20 mg/mL), 2 μL of EM, 1 μL of FD, 4 μL of primermixture (20 μM BIP/FIP, 10 μM LooP_B/Loop_F, and 2.5 μM B3/F3), 2 μL ofRNase Inhibitor (20 U/μl), 4 μL of HCV genotype 1 RNA, 1 μL of 80 μMoligo inhibitor and enough nuclease-free water to bring the volume to 40μL. The RNA was extracted from 140 μL of plasma (AcroMetrix® HCVGenotyping Panel) using QIAamp Viral RNA Mini Kit (Qiagen) with anelution volume of 60 μL. Loopamp® RT-LAMP mix was purchased from SAScientific. The solution was directly loaded onto SlipChip devices andsubject to heating at 63° C. for 50 minutes.

Example 6—Real-Time Bulk HCV Genotyping Results Using NASBA andRestriction Enzymes

Seven restriction enzymes—NheI, BsrBI, ApoI, BsrGI, NruI, BseYI andBstXI—were selected based on HCV sequence variation among differentgenotypes (Bsp681 is an isoschizomer of NruI having the same recognitionand cleavage specificity). A set of customized nucleic acid sequencebased amplification (NASBA) primers and molecular beacon probestargeting 5′UTR were designed; selected sequences are showed in Table 2,wherein bold type indicates the sequence of the bacteriophage T7DNA-dependent RNA polymerase promoter and stem sequences are indicatedwith underlines.

TABLE 2 NASBA primers and molecular beacon probe targeting 5′UTR. NameSequence 5′-3′ 5′UTR_P2_NASBA_HCV_forward GTCTAGCCATGGCGTTAGTA(Seq ID No: 2) 5′UTR_P1_NASBA_HCV_reverse_1 taatacgactcactatagggCAAGCACCCTATCAGGCAGTA (Seq ID No: 8) 5′UTR_P1_NASBA_HCV_reverse_2taattctaatacgactcact atagggCAAGCACCCTATCA GGCAGTA (Seq ID No: 9)5′UTR_probe_NASBA_HCV_sense_1 /FAM/CGTACGGTCTGCGGAA CCGGTGAGTACGTACG/BHQ1/ (Seq ID No: 10) 5′UTR_probe_NASBA_HCV_sense_2 /FAM/CGATCGAGCCATAGTGGTCTGCGGAACCGGTCGA TCG/BHQ1/ (Seq ID No: 3)

The cutting site of the restriction enzymes is included in the producedamplicon (231 pb) inside the primer region, so that, for example, theenzyme cuts the product during amplification and leads to inhibition ordelay of the reaction. Alignment of RNA sequences for genotypes 1, 2, 3and 4, priming and molecular beacon probe regions, and digestion sitesof NheI, BsrBI, ApoI, BsrGI, NruI (or Bsp681), BseYI and BstXI is shownin FIG. 13. In FIG. 13, Consensus genotype 1a (CON_GT1a); Consensusgenotype 1b (CON_GT1b); Consensus genotype 2a (CON_GT2a); Consensusgenotype 2b (CON_GT2b); Consensus genotype 3 (CON_GT3); Consensusgenotype 4 (CON_GT4); A: NheI; B: BsrBI; C: ApoI; D: BsrGI; E: NruI; F:BseYI; G: BstXI. Based on the specificity of the enzymes, the pattern ofNASBA-restriction enzyme (NASBA-RE) results were predicted as shown inFIG. 14. In FIG. 14, black circles represent negative NASBA reactions(inhibited reaction in the presence of the restriction enzyme shown onthe top of the column) and white circles represent positive NASBAreactions (non-inhibited reaction in the presence of the restrictionshown on the top of the column); each row represents a uniquecombination (pattern or fingerprint) of positive and negative NASBAreactions in the presence of different restriction enzymes associatedwith one HCV genotype. Multiple patterns of inhibition are possible forsome genotypes due to the existence of mutations and multiple sequenceswithin each genotype.

By using the proposed pattern, and based on multiple nucleotide sequencealignment obtained from HCV Los Alamos database, we analyzed thecoverage for Genotype 1 (subtypes 1a and 1b), Genotype 2, Genotype 3(subtype 3a) and Genotype 4. As shown in Table 3, in silico analysisshowed that 97.6% (n=1,269) of HCV sequences were correctly typed; 2%(n=26) of sequences are untyped; and 0.4% (n=5) of sequences aremistyped. In Table 3, N seq stands for the number of sequences; Pattern1, 2, 3 and 4 are described in FIG. 14; No Pattern includes thesequences that are not described by any of the predicted patterns inFIG. 14. Numbers of sequences and percentages in shaded boxes (Pattern 1GT1, Pattern 2 GT2, Pattern 3 GT3, and Pattern 4 GT4) describe genotypesunder the correct expected pattern.

TABLE 3 HCV genotype coverage based on predicted patterns. HCV GenotypeNo (subtype) N Seq Pattern 1 Pattern 2 Pattern 3 Pattern 4 Pattern GT1869 861 1 0 1 6 (1a + 1b) (99.1%) (0.1%) (0.0%) (0.1%) (0.7%) GT2 190 0181 0 0 9 (0.0%) (95.3%) (0.0%) (0.0%) (4.7%) GT3 134 2 0 125 1 6 (3a)(1.5%) (0.0%) (93.3%) (0.7%) (4.5%) GT4 107 0 0 0 102 5 (0.0%) (0.0%)(0.0%) (95.3%) (4.7%)

The time required for NASBA reaction to change from negative (belowintensity threshold) to positive (above intensity threshold) is shown inFIG. 15 and Table 4. The primer mix for 5′UTR NASBA reaction used inthis example includes: 5′UTR_P2_NASBA_HCV_forward,5′UTR_P1_NASBA_HCV_reverse_1 and 5′UTR_probe_NASBA_HCV_sense_1. Table 5shows real-time NASBA results with and without restriction enzymes forHCV genotyping with improved NASBA reaction. The primer mix for 5′UTRNASBA reaction used for these results includes:5′UTR_P2_NASBA_HCV_forward, 5′UTR_P1_NASBA_HCV_reverse_2 and5′UTR_probe_NASBA_HCV_sense_2. NruI was replaced by BstEII. Predicted(in silico) negative or delayed results are shown in bold.

TABLE 4 Real-time NASBA results with and without restriction enzymes forHCV genotyping. Restriction HCV RNA (Cq) Enzyme GT1 GT2 GT3 GT4 Non-RE(PC) 41.7 88.9 72.8 71.6 41.7 90.6 71.8 64.9 NheI neg NT NT neg neg NTNT neg BsrBI neg 78.3 neg neg neg 80.0 neg neg ApoI 38.2 94.6 NT NT neg91.8 NT NT BsrGI 43.6 76.3 76.5 NT 44.5 75.2 76.5 NT

TABLE 5 Real-time NASBA results with and without restriction enzymes forHCV genotyping with improved NASBA reaction. Restriction Time toPositive in minutes (SD) Enzyme GT1 GT2 GT3 GT4 Non-RE (PC) 26.6 (0.2)30.9 (0.7) 29.2 (1.2) 27.3 (0.1) NheI-HF Neg Neg 35.4 (7.1)  64.2 (20.3)BsrBI Neg 42.6 (1.5) Neg 42.8 (0.3) ApoI 27.1 (0.2) 34.8 (2.5) Neg 47.5(7.1) BsrGI 33.0 (1.2) 48.9 (1.8)  45.4 (17.6) 46.2 (6.3) BstEII 30.8(0.4) 44.5 (6.9) Neg 31.5 (1.3) BstXI 28.2 (0.8) 37.0 (0.2) Neg 34.4(3.3) Bsp681 Neg 40.2 (3.3) Neg 45.8 (0.1)

In the real-time experiment, each cycle was set to be 1 minute and thefluorescence intensity was measured at the end of each cycle. Due to thetime required for imaging (additional 12 seconds per cycle), the cyclenumbers did not reflect the absolute reaction time in the unit ofminute. The performance of this idea has been evaluated by testing NheI,BsrBI, ApoI and BsrGI against HCV genotypes 1, 2, 3 and 4. Preliminaryresults showed that real time NASBA reactions for HCV Genotype 1 areinhibited in combination with BsrBI, NehI, and are not inhibited in thepresence of ApoI and BsrGI. One of the replicates was also inhibited inthe presence of ApoI. For Genotype 2, no negative reactions wereobserved in the presence of BsrBI, ApoI and BsrGI. For Genotype 3,reaction with BsrBI was negative and positive with BsrGI, and forGenotype 4 the reaction was negative with BsrBI and NehI.

After optimization of primers/probe for 5′UTR HCV NASBA reaction theassay was evaluated with HCV GT1, GT2, GT3 and GT4 in the presence ofNheI-HF, BsrBI, ApoI, BsrGI, BstEII, BstXI and Bsp681 (restrictionenzymes were selected based on Table 5). Time to positive obtained inthe presence of the restriction enzymes were compared to a positivecontrol reaction (without restriction enzyme) for each HCV genotype(Table 5). Predicted (in silico) negative or delayed reactions are shownin bold in Table 5. Obtained reactions agreed with predicted results:GT1 amplification reactions were completely inhibited by NheI-HF, BsrBIand Bsp681; GT2 amplification reaction was completely inhibited byNheI-HF; GT3 amplification was completely stopped by BsrBI, ApoI,BstEII, BstXI and Bsp681; GT4 amplification reaction were stronglyinhibited by NheI-HF, BsrBI, ApoI, BsrGI, Bsp681. Presence ofnon-specific restriction enzymes also produced a delay in time topositive, but the extent of inhibition was less significant.

To amplify HCV viral RNA using a NASBA method on real-time PCR machinewithout restriction enzymes, the NASBA mix (NucliSens EasyQ Basic Kitv2, Biomerieux) was prepared as follows: 55 μL of Enzyme Diluent wereadded to an Enzyme Sphere and let sit for 20 min. The reagent mix wasprepared in a clean tube containing 80 μL of Reagent Sphere Diluent, 12μL NASBA Water, 16 μL KCl stock solution and the Reagent Sphere. Aftervortexing for 30 sec, 4.8 μL of vortexed NASBA forward primer (10 μMstock), 4.8 μL of vortexed NASBA reverse primer (10 μM stock) and 2.4 μLof vortexed NASBA probe (10 μM stock) were added to the reagent mix. Thesolution was split into 0.2 mL PCR tubes (10 μL each) and 4 μL of HCVRNA (sample) or nuclease-free water (non-template control) were loadedand incubated at 65° C. for 5 min Five μL of Enzyme solution (aftergently flicking it to mix) and 1 μL of nuclease-free water were added toeach PCR tube. The solution was split into 10 μL each and loaded into 2wells on a Eco real-time PCR (Illumina, CA) plate and heated at 41° C.for 120 min.

To amplify HCV viral RNA using a NASBA method a on real-time PCR machinein the presence of restriction enzyme, the NASBA mix (NucliSens EasyQBasic Kit v2, Biomerieux) was prepared as follows: 55 μL of EnzymeDiluent were added to an Enzyme Sphere and let sit for 20 min. Thereagent mix was prepared in a clean tube containing 80 μL of ReagentSphere Diluent, 12 μL NASBA Water, 16 μL KCl stock solution and theReagent Sphere. After vortexing for 30 sec, 4.8 μL of vortexed NASBAforward primer (10 μM stock), 4.8 μL of vortexed NASBA reverse primer(10 μM stock) and 2.4 μL of vortexed NASBA probe (10 μM stock) wereadded to the reagent mix. The solution was split into 0.2 mL PCR tubes(10 μL each) and 4 μL of HCV RNA (sample) or nuclease-free water(non-template control) were loaded and incubated at 65° C. for 5 min.Five μL of Enzyme solution (after gently flicking it to mix) and 1 μL ofdiluted RE (20 fold diluted from purchased stock solution) were added toeach PCR tube. The solution was split into 10 μL each and loaded into 2wells on an Eco real-time PCR (Illumina, CA) plate and heated at 41° C.for 120 min.

Furthermore, a Nokia 808 Pureview cell phone was used to imagemicrowells of a multivolume device (see, e.g., Feng Shen, Bing Sun,Jason E. Kreutz, Elena K. Davydova, Wenbin Du, Poluru L. Reddy, Loren J.Joseph, and Rustem F. Ismagilov, “Multiplexed Quantification of NucleicAcids with Large Dynamic Range Using Multivolume Digital RT-PCR on aRotational SlipChip Tested with HIV and Hepatitis C Viral Load,” JACS2011 133: 17705-17712) containing NASBA amplification product. This cellphone features a CMOS sensor with a Xenon flash. The Nokia 808 uses a1/1.4-inch 41-megapixel sensor with a pixel size of 1.4 μm. Cell phoneimaging was performed with a painted shoebox painted black inside. Allimages were taken using the standard cell phone camera application. Thewhite balance was set to automatic, the ISO was set at 800, the exposurevalue was set at +2, the focus mode was set to “close-up,” and theresolution was adjusted to 8 MP.

Example 7—Real-Time Bulk HCV Genotyping and Subtyping Using NASBA andRestriction Enzymes

14 restriction enzymes—AlwI, ApoI, BseYI, BsiEI, BsmAI, BsrBI, BsrGI,BsrI, BstEII, BstXI, BtsCI, HinfI, NheI and NruI—were selected for HCVgenotyping (genotypes 1, 2, 3, 4, 5 and 6) and subtyping. The presenceof target sequences for these restriction enzymes have been testedwithin the amplicon generated with the 5′UTR NASBA primers described inExample 6 and against a sequence alignment (n=1622) obtained from theLos Alamos HCV database. Results obtained by in silico analysis areshown in Table 6. In Table 6, the number of cutting sites perrestriction enzyme against HCV sequences are represented as percentage,numbers in shaded boxes represent >70% coincidence. Included areGenotype 1 (GT1): subtype 1a (GT1a), subtype 1b (GT1b) and other GT1subtypes (GT1nonAB); genotype 2 (GT2); Genotype 3 (GT3): subtype 3a(GT3a), subtype 3b (GT3b), subtype 3k (GT3k) and other GT3 subtypes(GT3nonABK); genotype 4 (GT4); genotype 5 (GT5); genotype 6 (GT6); N seqstands for the number of analyzed HCV sequences.

HCV NASBA primers and molecular beacon probes were also designed in COREand NS5B regions for subtyping purposes; examples are shown in Table 7,Table 8, and Table 9. In Table 7, Table 8, and Table 9, bold typeindicates the sequence of the bacteriophage T7 DNA-dependent RNApolymerase promoter, stem sequences are indicated with underlines, Yrepresents C or T, R represents A or G, and I represents inosine.

TABLE 6 Percentage of restriction enzyme cutting site per HCVgenotype/subtype within 5′UTR NASBA amplicon. HCV Genotype/ Restrictionenzymes Subtype N seq AlwI ApoI BseYI BsiEI BsmAI BsrBI BsrGI BsrIBstEII BstXI BtsCI HinfI NheI NruI GT1a 504 30.8 0.2 0.0 98.6 12.1 100.00.0 0.2 0.0 0.0 1.4 1.8 99.6 99.6 GT1b 365 88.5 0.0 0.0 94.5 96.4 99.50.0 0.5 0.0 0.3 4.4 1.1 99.7 99.5 GT1nonAB 29 48.3 17.2 0.0 93.1 27.6100.0 3.4 0.0 0.0 0.0 6.9 20.7 100.0 100.0 GT2 190 3.2 0.0 2.1 0.0 0.52.1 0.5 97.9 0.0 1.6 0.0 1.1 96.8 0.0 GT3a 134 3.7 97.0 96.3 1.5 2.299.3 0.0 0.7 94.0 96.3 3.0 97.8 3.0 99.3 GT3b 25 0.0 96.0 0.0 20.0 0.0100.0 0.0 0.0 0.0 0.0 80.0 96.0 0.0 100.0 GT3k 23 0.0 100.0 0.0 0.0 91.3100.0 0.0 0.0 0.0 0.0 0.0 100.0 100.0 95.7 GT3nonABK 21 9.5 81.0 14.314.3 19.0 100.0 0.0 0.0 85.7 14.3 0.0 100.0 14.3 100.0 GT4 107 17.8 87.90.0 13.1 18.7 100.0 70.1 0.0 0.0 0.0 82.2 86.9 97.2 80.4 GT5 52 1.9 1.90.0 17.3 98.1 100.0 0.0 0.0 0.0 0.0 82.7 5.8 100.0 100.0 GT6 172 71.50.0 0.0 60.5 73.8 89.5 1.2 0.6 0.0 0.6 29.1 30.2 99.4 77.3

TABLE 7 NASBA primers and molecular beacon probes targeting NS5B. NameSequence 5′-3′ NS5B NASBA HCV ACGGAGGCTATGACCYGGTA forward primer_1(Seq ID No: 11) NS5B NASBA HCV CTTCACGGAGGCTATGAC forward primer_2(Seq ID No: 12) NS5B NASBA HCV aattctaatacgactcactatagggagaaggATreverse primer_1 GTTGCCTAGCCAGGARTT (Seq ID No: 13) NS5B NASBA HCVaattctaatacgactcactatagggagaaggAT reverse primer_2 IATGTTGCCTAGCCAGG(Seq ID No: 14) NS5B NASBA HCV FAM probe_1 CCTGCACCAGAATACGACTTGGAGCTCATAACGTGCAGGBHQ1 (Seq ID No: 15) NS5B NASBA HCVFAM CCTGCACTAACATCATGITCCTCCAAY probe_2 GTGTCGTGCAGGBHQ1 (Seq ID No: 16)

TABLE 8 NASBA primers and molecular beacon probes targeting CORE. NameSequence 5′-3′ CORE NASBA HCV AGGACGTYAAGTTCCCGGG forward primer_1(Seq ID No: 17) CORE NASBA HCV GATCGTTGGTGGAGTTTAC forward primer_2(Seq ID No: 18) CORE NASBA HCV TCCTAAACCTCAAAGAAAAAC forward primer_3(Seq ID No: 19) CORE NASBA HCV aattctaatacgactcactatagggagaaggGCreverse primer_1 CAAGGRTACCCGGGCTG (Seq ID No: 20) CORE NASBA HCVaattctaatacgactcactatagggagaaggTC reverse primer_2 RTTGCCATAGAGGGGCC(Seq ID No: 21) CORE NASBA HCV aattctaatacgactcactatagggagaaggGGreverse primer_3 AGCCATCCYGCCCACCC (Seq ID No: 22) CORE NASBA HCVFAM CCTGCAAAGACTTCCGA probe_1 GCGGTCRCAACCTGCAGGBHQ1 (Seq ID No: 23)CORE NASBA HCV FAM CCTGCAAGGAAGACTTCC probe_2 GAGCGGTCRCATGCAGGBHQ1(Seq ID No: 24) CORE NASBA HCV FAM CCTGCAAAGACTTCCGAGC probe_3GGTCRCAACCTCGTGCAGGBHQ1 (Seq ID No: 25) CORE NASBA HCVFAM CCTGCAGGGTGTGCGCGCG probe_4 ACGAGGAAGACTGCAGGBHQ1 (Seq ID No: 26)

TABLE 9 NASBA primers and molecular beacon probes specificfor HCV NS5B GT1A and GT1B. Amplicon Name Sequence 5′-3′ size P1_GT1AAATTCTAATACGACTCACTATAGGGAAATCTACGG 120 bp ATAGCAAGTTRGC (Seq ID No: 27)P2_GT1A CCAAAGGCAGAAGAAAGTCA (Seq ID No: 28) Beacon_GT1A/FAM/CGCGATGGAGGTTAARGCRGCGGCGTATCGCG /BHQ1/ (Seq ID No: 29)P1_GT1B_set1 AATTCTAATACGACTCACTATAGGGAAACTCCAAG 130 bp TCGTATTCTGGTT(Seq ID No: 30) P2_GT1B_set1 CGACCTTGTCGTTATCTGTGA (Seq ID No: 31)Beacon_GT1B_set1 /FAM/CGCGATTTCACGGAGGCTATGACTAGGTATCG CG/BHQ1/(Seq ID No: 32) P1_GT1B_set2 AATTCTAATACGACTCACTATAGGGAAATGAATGA 107 bpTCTGAGGTAG (Seq ID No: 33) P2_GT1B_set2 TTCTTCTCCATCCTYMTA(Seq ID No: 34) Beacon_GT1B_set2 /FAM/CGCGATAARGCCCTRGAYTGYCAGATCTAATCGCG/BHQ1/ (Seq ID No: 35) P1_GT1B_set3AATTCTAATACGACTCACTATAGGGAAACACAACA 119 bp TTGGTANATTGACT(Seq ID No: 36) P2_GT1B_set3 GGTGAAHRCCTGGAAAKCRAA (Seq ID No: 37)Beacon_GT1B_set3_1 /FAM/CGCGATCACRGTCACYGAGARYGAYATCCGAT CGCG/BHQ1/(Seq ID No: 38) Beacon_GT1B_set3_2 /FAM/CGCGATCGACACCCGYTGYTTYGACTCAAGATCGCG/BHQ1/ (Seq ID No: 39) P1_GT1B_set4AATTCTAATACGACTCACTATAGGGAAAAAGTGG 110 bp YTCAATGGAGTA (Seq ID No: 40)P2_GT1B_set4 CAAGGATGATYCTGATGAC (Seq ID No: 41) Beacon_GT1B_set4/FAM/CGCGATCCCTYCTAGCNCAGGARCAACTGATC GCG/BHQ1/ (Seq ID No: 42)P1_GT1B_set5 AATTCTAATACGACTCACTATAGGGAAAGCTAGAA 113 bp GGATGGAGAAR(Seq ID No: 43) P2_GT1B_set5 GARACAGCTAGACACACT (Seq ID No: 44)Becon_GT1B_set5 /FAM/GCGATCGGCTAGGCAACATCATCATGATCGC/BHQ1/(Seq ID No: 45)

Example 8—Quantitative Nucleic Acid Detection by Loop-MediatedIsothermal Amplification (LAMP)

A Reverse-Transcription Loop mediated amplification (RT LAMP) assay wasconducted for quantitative isothermal detection of nucleic acids such asdetection of Hepatitis C viral (HCV) RNA. The test comprises at leastone nucleic acid primer set capable of detecting Hepatitis C viral (HCV)RNA in a LAMP based molecular test, the primer set being chosen from theprimer sets listed in Table 10. Each assay consists of a primer setincluding one pair of forward (FIP) and reverse (BIP) inner primers,forward (F3) and reverse (B3) outer primers. The assay can also includeloop forward (LF) and/or loop back (LB) primers to accelerate thereaction. HCV genotypes 1, 2, 3, 4, 5, 6, and 7 can be detected usingthe assay. The assay is applicable for studying a number of diseases,including but not limited to accurate HCV quantification using a digitalformat (i.e., confining single molecules into compartments andamplifying them separately) on a SlipChip device.

Primers for LAMP were designed to achieve improvements including ahigher melting temperature for reverse-transcription primers, weakenedloopF primer annealing to improve efficiency and delaying time toproduct signal, and positioning important-to-anneal fast primer parts(B1c and F1c) to be complementary to the secondary structures loop inRNA template to improve detection efficiency. HCV, like HIV, has a largevariety of genotypes and mutates rapidly due to the error-prone natureof the reverse transcriptase. As a result, it is beneficial for aquantification assay to be able to detect all the genotypes or genotypeswith high prevalence. To make the primer set general, the 3′ halves ofthe B3, F3, B2, F2 primers sequences and the 5′ halves of the B1c andF1c primers sequences were positioned to the most conserved positions inthe all HCV known sequences alignment. The primers were further made tobe universal and suitable to a widest known variety of HCV isolates, andare shown in Table 10, Table 11, and Table 12. FIG. 17 shows anillustration of one of the disclosed B side primers and primer partssequences variant aligned to one of the typical HCV sequences. FIG. 18shows an illustration of one of the disclosed F side primers and primerparts sequences variant aligned to one of the typical HCV sequences.

TABLE 10 A summary of basic and universal (containing Inosineas a general nucleic acid base pairer) primersdeveloped for efficient and specific detection of,for example, HCV RNA via RT-LAMP. Primer F3 FIP loopF (LF) basicCCTCCCGGGA TCCAAGAAAGGACCCGGTCTTTTTCT GTCCTGGCAAT GAGCCATAGGCGGAACCGGTGAGTAC TCCGGT (Seq ID (Seq ID No: 47) (Seq ID No: 46) No: 48)universal CCTCCCGGGA TCCAAGAAAGGACCCIGTCTTTTTCT TTICCGGIAATT GAGCCATAGGCGGAACCGGTGAGTAC CCGGT (Seq ID (Seq ID No: 49) (Seq ID No: 46) No: 50)Primer B3 BIP loopB (LB) basic GCACTCGCAA TTGGGCGTGCCCCCGCAAGTTTTTCACTGCTAGCCGA GCACCCTATC GTACCACAAGGCCTTTCGCGACC GTAGTGTTG (Seq ID(Seq ID No: 52) (Seq ID No: 51) No: 53) universal GCACTCGCAATTGGGCGTGCCCCCGCIAGATTTTTC CTGCTAGCCGA GCACCITATCAGTACCACAAGGCCITTCGCIACC GTAGIGTTG (Seq ID (Seq ID No: 55) (Seq IDNo: 54) No: 56,)

TABLE 11 A summary of additional FIP primers, designedin this case to compensate for a known HCVisolates of different subtypes/genotypes, via RT-LAMP detection.genotype FIP variant 1 TCCAAGAAAGGICCCIGTCTTTTT CTGCGGAACCGGTGAGTAC(Seq ID No: 57) 2 CCCAAGAAAGGICCCIGTCTTTTT CTGCGGAACCGGTGAGTAC(Seq ID No: 58) 3 TCCAATGGAAAGGICCCIGTCTTTTT CTGCGGAACCGGTGAGTAC(Seq ID No: 59) Some 4 and 6 TCCAAGAAAGGICCCIGTCTTTTTCTGCGGAACCGGTGAGTTC (Seq ID No: 60) Some 1 TCCAIGAAAGGACCCGGTCTTTTTCTGCGGAACCGGTGAGTAC (Seq ID No: 61)

TABLE 12 A summary of universal loopF (LF) primers,designed to compensate for known subtypes/genotypes sequence variations. Template consensus genotype LF primerACCGNAATTGCCAGGAC 1 GTCCTGGCAATTICGGT (Seq ID No: 62) (Seq ID No: 63)ACCGGAATTNCCGGNAA 2 and 1 TTICCGGIAATTCCGGT (Seq ID No: 64)(Seq ID No: 50) ACCGGAATNGCNGGGNN 3 and 4 IICCCIGCIATTCCGGT(Seq ID No: 65) (Seq ID No: 66) ACCGGAATNGCNGGGGT AICCCIGCIATTCCGGT(Seq ID No: 67) (Seq ID No: 68)

Back side primers can comprise the following:

BIP: (Seq ID No: 69) 5′TTGGGCGTGCCCCCGCAAGttttCAGTACCACAAGGCCTTTCGCGACC 3′BIP primer comprises of the B2 and B1c parts, which may be connecteddirectly, or through any linker sequence, including but not limited totttt.

B2 part of BIP: (Seq ID No: 70)the core sequence is 5′-CAGTACCACAAGGCCTTTCGCGACC- 3′As a B2 part of BIP primer, an oligonucleotide is used comprising atleast 5 consecutive nucleotides of the nucleotide sequenceCAGTACCACAAGGCCTTTCGCGACC (Seq ID No: 70).

B1c part of BIP: (Seq ID No: 71)the core sequence is 5′-TTGGGCGTGCCCCCGCAAG-3′Variations of the B1c part of BIP incorporation of inosin, LNA or BNAmodified, and other modified bases.

(Seq ID No: 72) loopB: 5′ CTGCTAGCCGAGTAGTGTTG 3′A loopB element may or may not be present in the amplification reaction.Variations of loopB include incorporation of inosine, LNA or BNAmodified, and other modified bases. As a loopB primer an oligonucleotidecan be used comprising at least 5 consecutive nucleotides of thenucleotide sequence CTGCTAGCCGAGTAGTGTTG (Seq ID No: 72).

(Seq ID No: 51) B3: 5′-GCACTCGCAAGCACCCTATC-3′B3 primer may or may not be present in 1-step RT-LAMP reactions. As a B3primer an oligonucleotide can be used comprising at least 5 consecutivenucleotides of the nucleotide sequence GCACTCGCAAGCACCCTATC (Seq ID No:51).

Forward side primers can comprise the following:

(Seq ID No: 46) F3 primer: 5′-CCTCCCGGGAGAGCCATAG-3′As a F3 primer an oligonucleotide can be used comprising at least 5consecutive nucleotides of the nucleotide sequence CCTCCCGGGAGAGCCATAG(Seq ID No: 46).

FIP primer: (Seq ID No: 47)5′-TCCAAGAAAGGACCCGGTCTTTTTCTGCGGAACCGGTGAGTAC-3′Variations on the FIP primer can include universal variants withinosines, or any other nucleotide bases instead of them are as follows:

(Seq ID No: 47) 5′-TCCAAGAAAGGACCCGGTC TTTTT CTGCGGAACCGGTGAGTAC- 3′(Seq ID No: 57) 5′-TCCAAGAAAGGICCCIGTC TTTTT CTGCGGAACCGGTGAGTAC-3′ (#1) (Seq ID No: 58)5′-CCCAAGAAAGGICCCIGTC TTTTT CTGCGGAACCGGTGAGTAC- 3′ (#2)(Seq ID No: 59) 5′-TCCAATGGAAAGGICCCIGTC TTTTT CTGCGGAACCGGTGAGTAC-3′ (#3) (Seq ID No: 60)5′-TCCAAGAAAGGICCCIGTC TTTTT CTGCGGAACCGGTGAGTTC- 3′ (#4 for some #4,6)(Seq ID No: 61) 5′-TCCAI-GAAAGGACCCGGTC TTTTT CTGCGGAACCGGTGAGTAC-3′(#5 for some #1)The FIP primer comprises of the F2 and F1c parts, which may be connecteddirectly, or through any linker sequence, including but not limited tottttt.

F2 part of FIP: (Seq ID No: 73)the core sequence is 5′-CTGCGGAACCGGTGAGTAC-3′,Variations of F2 can include incorporation of inosin, LNA or BNAmodified, and other modified bases. As a F2 part of FIP primer anoligonucleotide can be used comprising at least 5 consecutivenucleotides of the nucleotide sequence 5′ CTGCGGAACCGGTGAGTAC 3′ (Seq IDNo: 73).

F1c part of FIP: (Seq ID No: 74)the core sequence is 5′-TCCAAGAAAGGACCCGGTC-3′,As a F1c part of FIP primer an oligonucleotide can be used comprising atleast 5 consecutive nucleotides of the nucleotide sequenceTCCAAGAAAGGACCCGGTC (Seq ID No: 74) Loop F primers (LF): LF may or maynot be used in the amplification reaction. Some of LF variants used are:

(Seq ID No: 48) 5′GTCCTGGCAATTCCGGT 3′ (Seq ID No: 75)5′TCGTCCTGGCAATTCCG 3′ (Seq ID No: 48) 5′ GTCCTGGCAATTCCGGT 3′Variations of LF can include but are not limited to incorporation ofinosine, LNA or BNA modified, and other modified bases. As a LF primeran oligonucleotide can be used comprising at least 5 consecutivenucleotides of the nucleotide sequence TCGTCCTGGCAATTCCG (Seq ID No:75).

In addition, variations of all the mentioned primers and primer partscan include but are not limited to incorporation of inosine, LNA or BNAmodified, and other modified bases; changing up to 20% of the bases forthe other nucleotides, including inosine, dUTPs, LNA or BNA modifiedbases, RNA bases, abased nucleotides or any nucleotide analogs; shiftingor shortening the primer or primer part up to 7 bases counting fromeither it's 5′ or 3′ ends, or both; and simple elongating the primer.The primers were designed based on HCV genotype 1a, but aftermodification it can be used to detect all the major genotypescirculating in the US as well as other nucleic acids.

LAMP was conducted in a digital format (e.g., confining single moleculesinto compartments and amplifying them separately) on a SlipChip devicecomprising 1280 wells. FIG. 19 shows results for the number of positivewells versus time, from one step dRT-LAMP HCV RNA detection withreal-time tracking of the 1280 wells' intensity over time. The reactionwas done on standard fresh HCV RNA quantified with dRT-PCR, in apresence of total RNA extracted from human blood plasma, in 1× finalconcentration in reaction mixture. ˜250 HCV RNA were loaded, copiesquantified with RT-PCR. FIG. 20 shows results for the signal from eachwell versus time, from one step dRT-LAMP HCV RNA detection withreal-time tracking of the 1280 wells' intensity over time. At 50minutes, 128 positive counts had been observed out of an estimated total133+/−11 viral copies loaded and quantified with RT-PCR. FIG. 21 showsan image of a SlipChip device with results from one step dRT-LAMP HCVRNA detection. At 50 minutes, 99 positive counts are visible out of anestimated total 133+/−11 viral copies loaded, quantified with RT-PCR.FIG. 22 shows results for the number of positive wells versus time, fromone step dRT-LAMP HCV RNA detection with real-time tracking of the 1280wells' intensity over time. Reaction was done on standard fresh HCV RNAquantified with dRT-PCR, ˜133 HCV RNA copies were loaded (+/−˜11copies). At 50 minutes, 111 copies were detected in a first experiment(FIG. 22A) 111 and 134 copies were detected in a second experiment (FIG.22B).

Example 9—Real-Time Digital RT-LAMP/Restriction Enzyme (RT-LAMP/RE)Assay for HCV Genotyping

Real-time digital RT-LAMP/restriction enzyme (RT-LAMP/RE) experimentswere performed with HCV Genotype 1 (GT1) RNA using BsrBI as therestriction enzyme. RT-LAMP primers are shown in Table 13. HCV GT1isolate was obtained commercially and sequenced after RNA purificationto confirm the genotype assignment; sequencing results for HCV RNApurified from the isolates is shown in Table 14.

TABLE 13 Sequence of primers used in RT-LAMP. primer sequence (5′-3′) F3CCTCCCGGGAGAGCCATAG (Seq ID No: 46) HPTCCAAGAAAGGACCCIGTCTTTTTCTGCGGAACCGGTGAGTAC (Seq ID No: 49) LFTTICCGGIAATTCCGGT (Seq ID No: 50) B3 GCACTCGCAAGCACCITATC(Seq ID No: 54) BIP TTGGGCGTGCCCCCGCIAGATTTTTCAGTACCACAAGGCCITT CGCIACC(Seq ID No: 55) LB CTGCTAGCCGAGTAGIGTTG (Seq ID No: 56)

TABLE 14 Sequencing results for HCV RNApurified from purchased isolates. Genotype 1TCGTGCAGCCTCCAGGACCCCCCCTCTCGGGAGAGCCATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCAGGACGACCGGGTCCTTTCTTGGATCAACCCGCTCAATGCCTGGAGATTTGGGCGTGCCCCCGCGAGACTGCTAGCCGAGTAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCTCGGGAGGT (Seq ID No: 76) Genotype 2TCGTACAGCCTCCAGGCCCCCCCCTCCCGGGAGAGCCATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCGGGAAGACTGGGTCCTTTCTTGGATAAACCCACTCTATGCCCGGCCATTTGGGCGTGCCCCCGCAAGACTGCTAGCCGAGTAGCGTTGGGTTGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT (Seq ID No: 77) Genotype 3TCGTGCAGCCTCCAGGATCCCCCCTCCCGGGAGAGCCATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATCGCTGGGGTGACCGGGTCCTTTCTTGGAGCAACCCGCTCAATACCCAGAAATTTGGGCGTGCCCCCGCGAGATCACTAGCCGAGTAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT (Seq ID No: 78) Genotype 4TTGTACAGCCTCCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATCGCCGGGATGACCGGGTCCTTTCTTGGATAAACCCGCTCAATGCCCGGAAATTTGGGCGTGCCCCCGCAAGACTGCTAGCCGAGTAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGGGAGGT (Seq ID No: 79)

BsrBI cuts dsDNA at sequences CCGCTC, and this sequence exists in theRT-LAMP amplicon of GT1 RNA. With negative control experiments, thehighest possible BsrBI concentration that did not trigger ab initio DNAsynthesis within the time of interest under reaction conditions wasidentified, as shown in FIG. 23. The concentration was determined byperforming a restriction enzyme dilution experiment in the presence ofall RT-LAMP components except HCV RNA and choosing the concentration forwhich ab initio synthesis was not observed within 50 min. Columnsrepresent time to positive (ttp) caused by ab initio DNA synthesis anderror bars stand for standard deviation. RT-LAMP reactions wereperformed in the absence of HCV RNA and in the presence of threedifferent dilutions (100-fold, 200-fold and 300-fold) of NheI (grey),BsrBI (striped), and BstNI (white). Horizontal solid line shows the ttpthreshold set for analysis (50 min). In the experiments reported in thispaper, 200-fold RE dilution was used because 100-fold dilution was notenough to remove the influence of ab initio DNA synthesis within 50 min.

A SlipChip microfluidic device was used to compartmentalize the reactionmixture, as shown in FIG. 24. Schematic drawings show the layout of topand bottom piece of the entire device on the right and a zoomed-inregion (black box) on the left (FIG. 24A), the relative position of twopieces when they are aligned to allow the loading of solution throughthe channel (FIG. 24B), and the relative position of two pieces whenthey are slipped to separate droplets from one another and formcompartments (FIG. 24C). The progress of amplification was monitored foreach single molecule using a CCD-based imaging system, with resultsshown in FIG. 25. FIG. 25A shows 1280 fluorescence traces for theRT-LAMP amplification process of all the wells on a SlipChip device(solid lines) and normalized averaged fluorescence curve in bulk (dashedline) in the absence of restriction enzymes. FIG. 25B shows traces fordigital (solid lines) and for bulk (dashed line) in the presence ofrestriction enzyme BsrBI. Horizontal solid lines indicate the thresholdlevels to consider a well positive. Vertical solid lines show the meanof the time-to-positive distribution. FIG. 25C shows the change ofcumulative counts over time for wells exceeding the threshold in FIG.25A, (upper five lines), and FIG. 25B (lower lines). The two bars belowthe x-axis show time-to-positive for real-time bulk experiments, thewidths of which stand for standard deviation for the bulk assay (n=5)(left line for FIG. 25A results, right line from FIG. 25B results). Evenin the amplification reaction in the absence of the restriction enzyme,significant heterogeneity was observed among rates of amplification ofdifferent molecules (FIG. 25A). Addition of BsrBI did not abolish thisheterogeneity (FIG. 25B). On average, even though the rates of thereactions decreased upon addition of BsrBI, the shift in reaction times(approximately 5 min, for the first well that turned positive) was smallrelative to the width of the distribution of the reaction times (over 30min). On the other hand, the fate of single-molecule amplification didchange significantly upon addition of BsrBI: ˜10-fold fewer moleculesgave rise to successful amplification (with a p-value of 0.00033),indicating that in digital RT-LAMP, BsrBI affects fate more than itaffects rate. FIG. 26 shows a histogram of real-time, single-moleculedigital RT-LAMP/RE experiments for HCV GT1 RNA; the graph shows thechange of rate for positive wells in the absence of restriction enzymeand in the presence of BsrBI; the two bars below the x-axis showtime-to-positive for real-time bulk experiments, the widths of whichstand for standard deviation for the bulk assay (n=5) (left arrow forabsence of restriction enzyme, right arrow for presence of restrictionenzyme).

The same competition experiments were performed in a bulk real-timeformat using an RNA concentration of ˜3.3×105 copies/mL (estimated basedon digital RT-LAMP results), equivalent to the concentration of a singlemolecule in a 3 nL well. Without BsrBI, the reaction in this bulkexperiment was approximately 5 min faster than the mean amplificationtime in the corresponding digital experiment (FIG. 25A); it was closerto the time of the amplification of the first molecule (approximately 2min slower) (FIG. 25C). Upon addition of BsrBI, the bulk reaction showedincreased variance and slowed down by Δtb=4.9±1.9 min (FIG. 25C); thisdelay was similar to the delay of the time-to-positive of the firstmolecule in the digital format, Δtd=4.2±1.1 min (FIG. 25C). These datasuggest that once exponential amplification of some molecules takes off,this process dominates the reaction mixture and is not affected by theamplification of the molecules that amplify later in the digitalformat—the bulk reaction has ended by then. In other words, the bulkexperiment is dominated by the rate of amplification of the earliestmolecules, and not sensitive to the fate of the rest of the molecules.FIG. 27A shows real-time RT-LAMP curves for GT1 in the absence ofrestriction enzyme (positive control); FIG. 27B shows real-time RT-LAMPcurves for GT1 in the presence of BsrBI.

Based on consensus obtained by aligning sequences of each genotypeobtained from Los Alamos National Laboratory (LANL), three restrictionenzymes thermostable under RT-LAMP conditions were chosen to target thesequence differences between these four genotypes within the RT-LAMPamplicon. NheI-HF (targeting GCTAGC) should recognize genotypes 1, 2,and 4; BsrBI (targeting CCGCTC) should recognize genotypes 1, 3, and 4;and BstNI (targeting CCWGG) should recognize only GT1. These predictionsare illustrated schematically in FIG. 28A, where black boxes representpredicted positive signal (amplification) and empty boxes representpredicted negative signal (inhibition). In FIG. 28, the first column inboth sections represents the positive control in the absence ofrestriction enzyme and the following three columns indicate experimentswith different restriction enzymes; each row represents a genotype (GT)of HCV RNA. Under LAMP conditions, these three enzymes remained activeand sequence specific, as shown in FIG. 29A with gel electrophoresis andrepresented schematically in FIG. 29B. In FIG. 29A, lanes 1, 6, 11, 16and 21 are 100 bp DNA ladders; lanes 2-5 are positive control, NheI-HFdigestion product, BsrBI digestion product, and BstNI digestion productfor genotype 1, respectively; lanes 7-10 are positive control and 3restriction enzyme digestion products for genotype 2; lanes 12-15 arefor genotype 3; and lanes 17-20 for genotype 4. The specificity ofrestriction enzyme to different genotypes are the same as predicted inFIG. 28A: for genotype 1, all 3 restriction enzymes digested theproduct; for genotype 2 only NheI-HF digested the product; for genotype3 only BsrBI digested the product, and for genotype 4 both NheI-HF andBsrBI digested the product.

For each genotype, four digital experiments were performed: one positivecontrol without restriction enzymes, and three experiments with onerestriction enzyme each. The positive control also provided ameasurement of the viral load and validation for performing digitalexperiments, with results shown in Table 15. The experimental results(FIG. 28B) agreed with the inhibition pattern predicted (FIG. 28A)Amplification of GT1 was inhibited by all three restriction enzymes;amplification of GT2 was inhibited by NheI-HF only; amplification of GT3was inhibited by BsrBI; and amplification of GT4 was inhibited byNheI-HF and BsrBI. The fate of molecules for each combination wasdependent somewhat on the restriction enzyme being used, but in allcases the inhibition was strong and statistically significant (FIG.30B).

TABLE 15 Statistical analysis of digital counts obtained in positivecontrols for RT-LAMP of different HCV genotypes. Distribution of numbersof amplifiable RNA molecules in wells calculated based on observeddigital counts and Poisson statistics. HCV RNA GT1 GT2 GT3 GT4 Averagecounts 190 96 130 129 Standard deviation 44 23 18 5 Poisson estimate ofzero 1090 1184 1150 1151 amplifiable molecules per well Poisson estimateof one 175 92 123 122 amplifiable molecule per well Poisson estimate oftwo 14 4 7 6 amplifiable molecules per well Poisson estimate of three 10 0 0 amplifiable molecules per well Poisson estimate of average 0.160.078 0.11 0.11 amplifiable molecules per well

The performance of this HCV genotyping approach in a real-time bulkformat (FIG. 30A) was then compared to that in a digital format (FIG.30B). Experimental repeats were performed on different days to ensurethese experiments were not merely technical replicates. Both formatsagreed with the prediction shown in FIG. 24A. In the digital format(FIG. 30B), reactions with restriction enzymes specific to the genotypeshowed counts reduced by at least 10 fold, giving statisticallysignificant results (p<0.022). In the bulk format (FIG. 30A), reactionswith restriction enzymes that are specific to the genotype were alldelayed by a certain amount of time ranging from 2 min (˜10% relative totime-to-positive of positive control) to 20 min (˜100% relative totime-to-positive of positive control). Acceptable p-values were obtainedfor three of the four genotypes (p=0.079 for GT2 and p<0.032 forothers). As the strength of inhibition by the restriction enzymeincreased, (e.g., NheI-HF in FIG. 30B), in digital, lower counts andsmaller p-values were observed.

Results from the SlipChip device were also imaged on a cell phone, asshown in FIG. 31. Positive wells were clearly distinguished fromnegative wells, indicating the compatibility of this assay with cellphone imaging. The combinations of RNA genotypes and REs are GT3 withoutrestriction enzyme (FIG. 31A), GT3 with BsrBI (FIG. 31B); GT1 with BsrBI(FIG. 31C); and GT3 with BstNI (FIG. 31D).

Details for conducting experiments as described in Example 9 are asfollows: All solvents and salts purchased from commercial sources wereused as received unless otherwise stated. The Loopamp® RNA amplificationkit and the Loopamp® Fluorescent Detection Reagent kit were purchasedfrom SA Scientific (San Antonio, Tex., USA). The LoopAmp® RNAamplification kit contains 2× Reaction Mix (RM) (40 mM Tris-HCl pH 8.8,20 mM KCl, 16 mM MgSO4, 20 mM (NH4)2504, 0.2% Tween20, 1.6 M Betaine anddNTPs 2.8 mM each), Enzyme Mix (EM) (mixture of Bst DNA polymerase andAMV reverse transcriptase), and distilled water (DW). Loopamp®Fluorescent Detection Reagent kit contains Fluorescent Detection Reagent(FD) (including calcein). SsoFast EvaGreen Supermix (2×) was purchasedfrom Bio-Rad Laboratories (Hercules, Calif.). Bovine serum albumin (BSA)was purchased from Roche Diagnostics (Indianapolis, Ind.). Allrestriction enzymes were purchased from New England Biolabs (Ipswich,Mass.). All primers were ordered from Integrated DNA Technologies(Coralville, Iowa). Mineral oil (DNase, RNase, and Protease free),tetradecane, and DEPC-treated nuclease-free water were purchased fromFisher Scientific (Hanover Park, Ill.). Dichlorodimethylsilane waspurchased from Sigma-Aldrich (St. Louis, Mo.). AcroMetrix® HCV-s paneland AcroMetrix® HCV High Control and EXPRESS One-Step SYBR GreenERUniversal were purchased from Life Technologies (Grand Island, N.Y.).Genotype 3 and genotype 4 HCV viral isolates were purchased fromSeraCare Life Sciences (Gaithersburg, Md.). Nucleic acid extraction kitQIAamp Viral RNA Mini kit was purchased from QIAGEN (Inc, Valencia,Calif., USA) PCR Mastercycler and in situ adapter were purchased fromEppendorf (Hamburg, Germany) Eco real-time PCR system was purchased fromIllumina, Inc. (San Diego, Calif.). Photomasks were designed in AutoCAD2013 and ordered from CAD/Art Services, Inc. (Bandon, Oreg.). Soda-limeglass plates coated with layers of chromium and photoresist were orderedfrom the Telic Company (Valencia, Calif.). Sanger sequencing service wasprovided by Laragen, Inc. HCV sequences were extracted from Los Alamosdatabase and aligned with Geneious software.

4 different HCV genotypes were assayed. Genotypes 1 and 2 were purchasedfrom Acrometrix Corporation (Benicia, Calif., USA) and genotypes 3 and 4from SeraCare Life Sciences (Milford, Mass., USA). Genotype and viralload information was provided by these companies: viral load of 2.5×107IU/mL for GT1, 1.1×106-3.4×106 IU/mL for GT2, 5.7×106 IU/mL for GT3, and4.97×106 IU/mL for GT4. The genotype information was also provided bythe companies and we confirmed the genotype by sequencing andphylogenetic analysis. The presence of targeted single-nucleotidepolymorphisms or SNPs (restriction enzyme cutting sites) was confirmedby manual inspection of the sequencing chromatograms. RNA was extractedusing the QIAamp Viral RNA Mini Kit (QIAGEN Inc, Valencia, Calif., USA)according to the manufacturer's instructions, using 200 μL of plasma andeluting the resulting nucleic acid extraction in 60 μL of elutionbuffer. Nucleic acid extractions were analyzed immediately or stored at−80° C. until further analysis. To amplify HCV viral RNA, the RT-PCR mixcontained the following: 20 μL of 2× SsoFast Evagreen SuperMix, 1 μL ofEXPRESS SYBR GreenER RT module, 1 μL of each primer (10 μM), 2 μL oftemplate, and enough nuclease-free water to bring the volume to 40 μL.The reverse transcription was carried out at 50° C. for 15 min, followedby 2 min of reaction termination at 95° C. The amplification step wasperformed by 40 cycles of the following conditions: 95° C. for 15seconds, 55° C. for 1 min and 72° C. for 1 min. The dendogram wasconstructed by alignment of the 222 nucleotide sequences within the5′UTR region of HCV based on the UPGMA method under the Tamura-Nei model(bootstrap=1,000 replicates). Reference sequences from HCV strains(genotypes 1 to 4) were obtained from the Los Alamos HCV database. Toamplify HCV viral RNA using RT-LAMP on a real-time PCR machine, theRT-LAMP mix contained the following: 20 μL of 2× reaction mix (RM), 2 μLof enzyme mix (EM), 1 μL of fluorescent detection reagent (FD), 4 μL ofprimer mixture (20 μM BIP/FIP, 10 μM LB/LF, and 2.5 μM B3/F3), variousamounts of RNA template solution (2.86 μL GT1 RNA for FIG. 3, 2 μL10-fold diluted GT1 RNA and 2 μL RNA for all the other genotypes forFIGS. 4 and 5), and enough nuclease-free water to bring the volume to 40μL. The solution was split into 10 μL each and loaded into 3 wells onthe Eco real-time PCR plate and heated at 63° C. for 50 min. RT-LAMPreagents and FD were used as purchased from SA Scientific and used as itwas. To amplify HCV viral RNA using RT-LAMP in the presence of RE onreal-time PCR machine, the RT-LAMP mix contained the following: 20 μL ofRM, 2 μL of EM, 1 μL of FD, 4 μL of primer mixture (20 μM BIP/FIP, 10 μMLB/LF, and 2.5 μM B3/F3), various amounts of RNA template solution (2.86μL GT1 RNA for FIG. 3, 2 μL 10-fold diluted GT1 RNA and 2 μL RNA for allthe other genotypes for FIGS. 4 and 5), 4 μL 20-fold diluted RE (to makea 200-fold dilution in the final solution) and enough nuclease-freewater to bring the volume to 40 μL. RE was diluted in nuclease-freewater before immediately mixed with RT-LAMP reagents, and fresh dilutionwas made each time. The solution was split into 10 μL each and loadedinto 3 wells on the Eco real-time PCR plate and heated at 63° C. for 50min Bulk RT-LAMP/RE assays were carried out in an Eco Real-Time PCRSystem (Illumina, SD, USA) and data analysis was performed using EcoReal-Time PCR System Software (version 4.0). To determine thetime-to-positive (time required for the fluorescent signal to cross thethreshold), fluorescence intensity between 5 min and 15 min was used asthe baseline and the threshold value was set to be half height of themaximum intensity. For the single-volume 1280-well SlipChip, allfeatures were etched to a depth of 55 μm in soda lime glass to make thevolume of loading well equal to 3 nL. To amplify HCV viral RNA usingRT-LAMP method on real-time PCR machine, the RT-LAMP mix contained thefollowing: 20 μL of RM, 2 μL of EM, 1 μL of FD, 4 μL of primer mixture(20 μM BIP/FIP, 10 μM LB/LF, and 2.5 μM B3/F3), 2 μL of BSA (20 mg/mL),various amounts of RNA template solution (2.86 μL GT1 RNA for FIG. 3, 2μL 10-fold diluted GT1 RNA and 2 μL RNA for all the other genotypes forFIGS. 4 and 5), 4 μL diluted RE if not for positive control, and enoughnuclease-free water to bring the volume to 40 μL. The solution wasloaded onto SlipChip and heated at 63° C. for 50 min on a custom-builtreal-time instrument. RT-LAMP reagents and FD were used as purchasedfrom SA Scientific. BSA was used as purchased from Roche Diagnostics.Experiments were performed on a Bio-Rad PTC-200 thermocycler with acustom machined block. The block contains a flat 3″×3″ portion ontowhich the devices are placed ensuring optimal thermal contact. Theexcitation light source used was a Philips Luxeon S (LXS8-PW30) 1315lumen LED module with a Semrock filter (FF02-475). Image Acquisition wasperformed with a VX-29MG camera and a Zeiss Macro Planar T F2-100 mmlens. A Semrock filter (FF01-540) was used as an emission filter. Imagesacquired were analyzed using self-developed Labview software. The datawere analyzed by first creating a binary mask that defined the locationof each reaction volume within the image. The masked spots were thenoverlaid on the stack of images collected over the course of theexperiment and the average intensity of each individual masked spot wastracked over the course of the stack. Background subtraction of thereal-time trace was performed by creating a least mean square fit ofeach individual trace. Threshold was then manually set at the halfheight of the averaged maximum intensity, and the time-to-positive ofeach reaction was then determined as the point at which the real-timecurve crossed the defined threshold. Cell phone imaging white balancewas set to automatic, the ISO was set at 800, the exposure value was setat +2, the focus mode was set to “close-up”, and the resolution wasadjusted to 8 MP. To test the specificity and activity of RE at thecondition for RT-LAMP, we first prepared RT-LAMP product from HCV RNA ofgenotype 1, 2, 3, and 4, respectively. The amplification procedure wasthe same as described in above except that an additional 5 min at 85° C.was used to inactivate the polymerase. 2 μL RT-LAMP product was mixedwith 4 μL fresh RM, 3 μL nuclease-free water and 1 μL RE (or water fornon-RE control) and incubated at 63° C. for 30 min. The digestionproduct was analyzed on 1.2% agarose DNA gel stained with ethidiumbromide at 75 Volt for 40 min. To determine the restriction enzymeconcentration which did not trigger ab initio synthesis within 50 min,three dilutions (100-fold, 200-fold and 300-fold dilution in the finalmixture) of each RE were added to RT-LAMP mix containing the samecomponents as in the genotyping assay with the exception of HCV RNAtemplate that was replaced with nuclease-free water. RE was diluted innuclease-free water before immediately mixed with RT-LAMP reagents, andfresh dilution was made each time. The solution was split into 10 μLeach and loaded into 3 wells on the Eco real-time PCR plate and heatedat 63° C. for 96 min High-complexity molecular tests such ascommercially available HCV genotyping assays are not well suited forlimited-resource settings: for example, hybridization assays (RocheLINEAR ARRAY Hepatitis C Virus Genotyping Test, Siemens VERSANT HCVGenotype 2.0 assay (LiPA)) and hybridization followed by electrochemicalreadout (GenMark eSensor) assays start with a PCR step, take fromseveral hours up to one day, and require strict control of conditions;sequencing analysis is also slow and requires complex protocols andinstrumentation (TRUGENE HCV Genotype Test). Automated real-time RT-PCRwith Taqman probes (Abbott RealTime HCV Genotype II) is faster (˜5 hrs)but is still too complex and as a kinetic measurement not sufficientlyrobust for limited-resource settings.

Example 10—Modified NASBA with Oligonucleotide Modulator

To amplify HCV viral RNA using a usual NASBA protocol on a real-time PCRmachine without oligonucleotide modulator, the NASBA mix contained thefollowing: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of the nucleotidemix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and 10 μM DNAmolecular beacon), various amounts of RNA template solution, andnuclease-free water (to bring the volume to 15 μL). This mixture wasgently mixed and microcentrifuged for a few seconds, then P1 wasannealed by heating for 2 min at 65° C. and cooling 10 min at 41° C.(pre-incubation step) Immediately after the annealing, 5 μL of enzymemixture (NEC) was added to this mixture. The solution was loaded intotwo wells (9 μL each) of an Eco real-time PCR plate and incubated at 41°C. for 90 min while monitoring the fluorescent signal in one-minuteintervals. NASBA reagents were purchased from Life Sciences AdvancedTechnologies.

To amplify HCV viral RNA using a modified NASBA method on a real-timePCR machine without oligonucleotide modulator, the NASBA mix containedthe following: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of thenucleotide mix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and10 μM RNA molecular beacon), 0.6 μL of Hybridase Thermostable Rnase Hvarious amount of RNA template solution, and enough nuclease-free water(to bring the volume to 15 μL). This mixture was gently mixed andmicrocentrifuged for a few seconds, then P1 was annealed by heating for2 min at 65° C. and cooling 10 min at 41° C. (pre-incubation step).Immediately after the annealing 5 μL of enzyme mixture (NEC) was addedto this mixture. The solution was loaded into two wells (9 μL each) ofan Eco real-time PCR plate and heated at 41° C. for 90 min whilemonitoring the fluorescent signal in one-minute intervals. NASBAreagents were purchased from Life Sciences Advances Technologies andHybridase Thermostable Rnase H was purchased from Epicentre.

To amplify HCV viral RNA using a modified NASBA method on a real-timePCR machine with oligonucleotide modulator, the NASBA mix contained thefollowing: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of the nucleotidemix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and 10 μM RNAmolecular beacon), 0.5 μL of specific oligonucleotide modulator (10 μM),0.6 μL of Hybridase Thermostable Rnase H various amount of RNA templatesolution, and enough nuclease-free water (to bring the volume to 15 μL).The mixture was gently mixed and microcentrifuged for a few seconds,then P1 was annealed by heating for 2 min at 65° C. and cooling 10 minat 41° C. (pre-incubation step) Immediately after the annealing 5 μL ofenzyme mixture (NEC) was added to this mixture. The solution was loadedinto two wells (9 μL each) of an Eco real-time PCR plate and heated at41° C. for 90 min while monitoring the fluorescent signal in one-minuteintervals. NASBA reagents were purchased from Life Sciences AdvancesTechnologies and Hybridase Thermostable Rnase H was purchased fromEpicentre.

Table 16 shows a comparison between a regular NASBA reaction and themodified NASBA reaction as discussed above. Table 17 shows real-timeNASBA results with and without specific antisense oligonucleotidemodulators targeting HCV RNA template. HCV Genotype 1 (GT1) withoutantisense oligonucleotide modulator showed a Cq of 26.54; HCV GT1 in thepresence of specific GT1 oligonucleotide showed a Cq of 56.20, more than20 min delay; HCV GT1 in the presence of specific GT2 oligonucleotideshowed a Cq of 28.86, more than 2 min delay. Cq values are equivalent to1.2 min.

TABLE 16 Regular NASBA reaction compared to the modified NASBA reaction.regular modified Reagent NASBA NASBA NASBA Enzyme Cocktail 5.0 μL 5.0 μL3X NASBA Reaction buffer 6.7 μL 6.7 μL 6X Nucleotide Mix 3.3 μL 3.3 μLRNase H (5 U/μL) — 0.6 μL P1 (10 uM stock) 0.4 μL 0.4 μL P2 (10 uMstock) 0.4 μL 0.4 μL DNA molecular beacon (10 uM stock) 0.4 μL — RNAmolecular beacon (10 uM stock) — 0.4 μL RNA 2.5 μL 2.5 μL nuclease-freewater 1.3 μL 0.7 μL

TABLE 17 Specific inhibition with guide-RNAseH. Sample Cq (SD) HCV GT1 +RNAse H 26.54 (0.40) HCV GT1 + oligonucleotide modulator GT1 + RNase H56.20 (16.12) HCV GT1 + oligonucleotide modulator GT2 + RNase H 28.86(1.10)

FIG. 32 shows a comparison of NASBA reactions with DNA and RNA molecularbeacon before and after addition of extra amount of RNase H. FIG. 32Ashows the performance of a NASBA reaction using a DNA molecular beacon(dashed line) and RNA molecular beacon (solid line) with standardconcentration of RNase H, as provided from a commercial company. FIG.32B shows the performance of a NASBA reaction using a DNA molecularbeacon (dashed line) and RNA molecular beacon (solid line) withincreased concentration of RNase H. All 9 μL reactions containedapproximately 1,000 genomic copies of hepatitis C virus GT1. Eachexperimental condition represents a mean from triplicate reactions.NASBA reactions with RNA molecular beacon were faster than reactionswith DNA molecular beacon. In the presence of higher RNase Hconcentration and RNA molecular beacon efficiency of the reaction wasimproved, plateau was reached faster.

FIG. 33 shows results from a modified NASBA reaction. Modified NASBA asdescribed in Table 16 was performed while varying the finalconcentration of RNA molecular beacon in the mixture. Triplicatereactions showed that the measured time to positive (FIG. 33A) waseffected very slightly as the beacon concentration increased from 0.1 μMto 0.4 μM. In contrast, the endpoint fluorescent intensity of themolecular beacons (FIG. 33B) increased from 0.39 to 0.9.

Example 11—Restriction Enzyme (ApoI) Enhanced RNA NASBA

FIG. 34 shows results from experiments on the effect of preincubation onthe time to positive of restriction enzyme (ApoI) enhanced RNA NASBAcompared to regular NASBA. NASBA reagents were purchased from LifeSciences Advances Technologies. Restriction Enzyme ApoI was purchasedfrom New England Biolabs, and experiments were conducted under thefollowing conditions:

Pre-incubation+ApoI (FIG. 34A, first from left): NASBA mix containingthe following: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of thenucleotide mix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and10 μM DNA molecular beacon), and 2 μL HCV RNA GT1 (final volume of 14μL). The mixture was gently mixed and microcentrifuged for a fewseconds, then P1 was annealed by heating for 2 min at 65° C. and cooling10 min at 41° C. (pre-incubation step) Immediately after the annealing 5μL of enzyme mixture (NEC)+1 μL of ApoI (5-fold diluted in water fromoriginal stock) were added to this mixture. The solution was loaded intotwo wells (9 μL each) of an Eco real-time PCR plate and heated at 41° C.for 90 min while monitoring the fluorescent signal in one-minuteintervals;

Pre-incubation (FIG. 34A, second from left): NASBA mix containing thefollowing: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of the nucleotidemix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and 10 μM DNAmolecular beacon), and 2 μL HCV RNA GT1 (final volume of 14 μL). Themixture was gently mixed and microcentrifuge for a few seconds, then P1was annealed by heating for 2 min at 65° C. and cooling 10 min at 41° C.(pre-incubation step) Immediately after the annealing 5 μL of enzymemixture (NEC)+1 μL of distilled water were added to this mixture. Thesolution was loaded into two wells (9 μL each) of an Eco real-time PCRplate and heated at 41° C. for 90 min while monitoring the fluorescentsignal in one-minute intervals;

Ice+ApoI (FIG. 34A, third from left): NASBA mix containing thefollowing: 6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of the nucleotidemix (NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and 10 μM DNAmolecular beacon), and 2 μL HCV RNA GT1 (final volume of 14 μL). Themixture was gently mixed and microcentrifuge for a few seconds and kepton ice for 12 min, time equivalent to pre-incubation Immediately afterthe annealing 5 μL of enzyme mixture (NEC)+1 μL of ApoI (5-fold dilutedin water from original stock) were added to this mixture. The solutionwas loaded into two wells (9 μL each) of an Eco real-time PCR plate andheated at 41° C. for 90 min while monitoring the fluorescent signal inone-minute intervals;

Ice (FIG. 34A, fourth from left): NASBA mix containing the following:6.7 μL of 3× Reaction Buffer (NECB), 3.3 μL of the nucleotide mix(NECN), 1.2 μL of primer mixture (10 μM P1, 10 μM P2 and 10 μM DNAmolecular beacon), and 2 μL HCV RNA GT1 (final volume of 14 μL). Themixture was gently mixed and microcentrifuge for a few seconds and kepton ice for 12 min, time equivalent to pre-incubation Immediately afterthe annealing 5 μL of enzyme mixture (NEC)+1 μL of distilled water wereadded to this mixture. The solution was loaded into two wells (9 μLeach) of an Eco real-time PCR plate and heated at 41° C. for 90 minwhile monitoring the fluorescent signal in one-minute intervals.

The time to positive was reduced by the same degree via the addition ofApoI and the inclusion of a pre-incubation step; including both furtherreduced the time to positive (FIG. 34A). FIG. 34B shows the effect ofpre-incubation on the RNA product of restriction enzyme (ApoI) enhancedRNA NASBA reaction compared to regular NASBA as visualized by gelelectrophoresis. When the reaction is performed without pre-incubation,nonspecific products dominate the visible reaction product. Including apre-incubation step reduces this product to a single predominant band.In a similar manner, the addition of ApoI prevents the accumulation ofnonspecific product, to a greater degree. Each experimental conditionwas run in duplicate.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

What is claimed is:
 1. A method, comprising: providing a volumesuspected of containing a target nucleic acid; dispersing said volumeamong a plurality of areas, such that said plurality of areas comprisesa distribution of nucleic acids, and conducting an isothermal nucleicacid amplification reaction in said volume in the dispersed volume insaid plurality of areas in presence of a modulator comprising anengineered or non-natural sequence-specific nuclease selected from thegroup consisting of zinc-finger nuclease, transcription activator-likeeffector nuclease, meganuclease and RNA-guided Cas9 nuclease, theengineered or non-natural sequence-specific nuclease cleaving saidtarget nucleic acid within a region amplified by said isothermal nucleicacid amplification reaction.
 2. The method of claim 1, wherein saiddistribution generates digital nucleic acid amplification signals. 3.The method of claim 2, wherein said plurality of areas each comprises atmost one copy of said target nucleic acid.
 4. The method of claim 2,further comprising prior to the conducting, providing the modulator tosaid plurality of areas.
 5. The method of claim 1, wherein the providingcomprises providing a first volume comprising a first nucleic acid and asecond volume comprising a second nucleic acid, wherein the dispersingcomprises dispersing said first volume among a plurality of first areasand dispersing said second volume among a plurality of second areas, andwherein the conducting is performed in the dispersed first volume insaid plurality of first areas and in the dispersed second volume in saidplurality of second areas.
 6. The method of claim 5, wherein saidplurality of first areas each comprise at most one copy of said firstnucleic acid and said plurality of second areas each comprise at mostone copy of said second nucleic acid.
 7. The method of claim 5, furthercomprising prior to the conducting, providing the modulator to saidplurality of first areas or to said plurality of second areas.
 8. Themethod of claim 5, further comprising detecting a difference in saidisothermal nucleic acid amplification reaction between said firstnucleic acid and said second nucleic acid.
 9. The method of claim 8,wherein said difference is diagnostic of the presence of the targetnucleic acid within said first nucleic acid and said second nucleicacid.
 10. The method of claim 1, wherein modulation by the modulatorcomprises producing a difference in amplification efficiency.
 11. Themethod of claim 10, wherein the said distribution generates digitalnucleic acid amplification signals, wherein said difference inamplification efficiency produces a positive amplification signal in asubset of said plurality of areas.
 12. The method of claim 11, whereinsaid positive amplification signal in said subset of said plurality ofareas is diagnostic of the presence of said target nucleic acid withinsaid volume.
 13. The method of claim 1, wherein the target nucleic acidcomprises an HCV nucleic acid.
 14. The method of claim 13, wherein saidmethod generates a signal from which an HCV genotype can be determined.15. The method of claim 1, further comprising comparing results of saidisothermal nucleic acid amplification reaction to results of a controlisothermal nucleic acid amplification reaction carried out in theabsence of the modulator.
 16. The method of claim 1, wherein saidisothermal nucleic acid amplification reaction is selected from thegroup consisting of Recombinase Polymerase Amplification (RPA),Loop-mediated isothermal amplification (LAMP), Helicase-dependentamplification (HAD), Strand displacement amplification (SDA), Nucleicacid sequence based amplification (NASBA), and Nicking enzymeamplification reaction (NEAR).
 17. The method of claim 16, wherein saidisothermal nucleic acid amplification reaction is LAMP or NASBA.
 18. Themethod of claim 1, wherein the modulator is RNA-guided Cas9 nuclease.19. The method of claim 18, wherein the modulator further comprises acrRNA and a tracrRNA, the crRNA, tracRNA and Cas9 forming aCas9-crRNA-tracrRNA complex.